Run the math on whether the difference between the bonus and the equity matters to you. If it does, time to negotiate. Simply say "I took this job in consideration of the fact that you offered me a package with X, Y, Z, and 1% equity. Your letter indicates that 1% equity may be infeasible for legal reasons. I think we can come to a mutually beneficial resolution which compensates me adequately and addresses your concerns. The sale bonus you have proposed doesn't quite get us there. What else can you offer me?" (Feel free to give suggestions, but talk topics, not numbers. First rule of negotiation: the first guy to give a number loses. Which is good news for you, because you have already heard one number. I can guarantee you, you won't get any worse than that!)
It is not possible to stress this enough. People should print this out in 72pt font size and hang it over their bed.
("$20,000? Holy cow! That's more money than I've ever had in my whole life! I'll take it!" -- not what I said in response to what my professor thought I would consider a very tempting offer.)
Because you are so fixed on that first number, I simply pad my desired number and throw out that right away. Now you feel like you won because you talked me down from my already inflated number, and I feel the same because I knew it was inflated anyway.
Reality is I got exactly what I wanted.
I would take a second of silence, mentally repeat to myself "We are all businessmen here. What I am about to do is morally and socially acceptable. I need feel no shame about it.", and ask for more $WHATEVER. What is the worst thing that happens? They say no, we suffer 2 seconds of awkwardness, and I get the offer they just made me. Or they say yes, and I probably just bought myself a month's salary (and 3~5% compounding on it for every year of employment) for 5 seconds of work.
The tax issue may be real but workarounds include giving you a grant of options exercisable at current fair market value, which gives you the opportunity to get the 1% equity without taking any immediate tax hit (you would have to pay more for the equity at the time of exercise than founders did at the beginning, and your ultimate tax consequences would be more complicated than you would have gotten through a simple early-stage grant of, e.g., restricted stock with an 83(b) filing, but you could still profit significantly in a success case).
Can't comment on your specific situation but, over the years, I have frequently seen "string out" situations where companies used people while never intending to follow through on their promises. Legal remedies in this situation are limited in a practical sense, with fraud being very hard to prove (especially where proving intent to defraud is a requirement and where the written offer letter does not contain the item you claim they represented they would give you) and with such cases often taking a six-figure sum, and a year or more of miserable fighting, to process through to verdict.
On the other hand, many startups are notoriously slow to document things when the founders think of the legal stuff as simply being a process of "papering" things they know they all agree upon.
The important thing here is to push to get the equity grant documented in some form as quickly as possible. This will flush out the company's intentions now, when your risks are less, as opposed to later, when you might be so committed as to be trapped. Tax issues do come up in this context but have never stopped any early-stage deal (in my considerable experience with this issue) where the parties truly desire to implement it.
My opinion is much simpler. If verbal promises are being broken this early in your relationship you shouldn't take a job that specifically asks you to make sacrifices based on being invested in the company's success.
To me it's as simple as that. The very fact that you're asking yourself these questions is the best warning sign.
There are ways to grant equity without causing tax troubles for the recipient. If there weren't, how could the employees of any startup get equity?
They are not treating you as employee #1 of a startup. Therefore, you should treat them the same way you would treat Big Employer.
If he's a new employee he should give his company the benefit of the doubt for a short time. And use the time to demonstrate his value. The thing to avoid is a drawn out process where it isn't clear what constitutes a reasonable timeframe for getting this problem solved and so it always gets pushed back.
So get the milestones figured out. If now is not a convenient time, when is a convenient time? When you've been employed for three or six months? When the company hits major development or business milestones? If you can't get an oral commitment on this front I'd be concerned enough to look elsewhere.
Further, I'm concerned that they are not being honest with him (1% equity, oops maybe not). That doesn't mean he can't do business with them, but he should heavily discount the value of future promises.
Not being able to openly and honestly communicate the parameters of your deal, which is their responsibility if they're doing the hiring, is a very bad sign and doesn't bode well for the future of the company.
Especially when they realise they've given you an incorrect deal, or a deal they can't do, or whatever - the solution is not to quietly update the contract and push it across the table and hope you don't notice. The solution is of course to sit down and openly discuss the situation to make sure everyone you understand exactly what is going on, and why, then allow you to make your decision based on this new information.
If none of the founders are able to do this, or want to do this, this is a major red flag.
In this case, if a restricted stock grant is made, the grant is taxed at the fair market value of the stock on date of grant - this constitutes ordinary income to the recipient. An 83(b) filing in such case would only shelter the grant from further tax hits as it may vest down the road should the fair value of the stock go up even more by the time it reaches the various vesting points.
Thus, the basic point used in the illustration above is correct. There would be as much as $50K in taxable income realized in such a case.
You already have a value that you consider to be fair, and clearly you aren't receiving that. They need to know that you feel this way, exactly.
They may agree and choose to improve your situation, or they may disagree.
If they disagree then the choice is yours: accept their view unconditionally, or end the relationship and move on. Unfortunately, not everyone can always come to an agreement, but most employees use the fear of losing a job to accept things that they should never consider.