First, start actually printing out contracts to execute them. It's old fashioned, and you probably don't have a printer (Staples does). But it preserves your right to cross things out and makes it clear that there is an authoritative "wet ink" copy that you specifically agreed to, not some vague digital assent to whatever they sent.
Also get in the habit of initialing each page of a contract, regardless of whether there is a space asking you to or not. A lack of initials then becomes evidence that a given page is not from a contract you signed.
And you need to keep a copy of what you've executed for your own long-term records. It's ultimately your word against theirs. Yes, this is another pain in the ass for the average 20-something, but if you care about preserving your rights you have to play their shitty game.
Relatedly, I'd love to find (or design) some "legalhash" algorithm that would canonicalize typeset documents into a reliable digital hash. I'm imagining a small set of characters, all whitespace folded into a single space, etc. This would capture the legal intent but leave everything else behind (wouldn't work for contracts with diagrams etc). You'd then put the hash of the whole document on the signature/notarization page, to authenticate the prior pages.
Depending on the context, it's possible to just completely ignore them (eg a non-compete that a job wants you to sign after you've already been hired).
You can also directly ask for your changes, as discussed elsewhere.
Ultimately, if someone tries to spring an unreasonable contract of adhesion on you at the last minute, the right answer is to blame them for disrupting the negotiation. Tell them it's unacceptable for them to have wasted your time, and look around for a better option.
For example once when I was young I was hired by the following process. I see on the TV news that a chip fab I've worked in caught fire, damaging nearby buildings. There are a lot of fire engines but the blaze is under control. Then I get a phone call from a friend, "Mountbatten is on fire". "I saw that". "We're getting Zepler back tomorrow, once structural engineers sign off on it - can you be there 0900 sharp to salvage stuff and get the network back up?". "Can do. See you tomorrow".
No interview. No pieces of paper. No salary negotiation. But that's an employment contract, just some of the details not determined until later. I actually genuinely don't remember how long I worked that gig, it was a lot of fun although pretty different from what I do these days.
In court, forging evidence by relating a signature page to the wrong document so they can then lie to a court about it is not OK - their lawyers aren't going to want to have anything to do with that idea. Contrariwise, if you have an email back-and-forth, or even just a friend who remembers you talking about the change, you're in a good place because your story makes sense and the employer's story does not.
But mostly you aren't going to be in court. If you're confident the employer would try to actually fuck you over, and you're in the sort of work where you get to strike contract terms, walk away from that job. Nobody needs that.
In digital terms, it's easier just to amend the whole file.