Yeah, I wouldn't risk not using MICR ink just because you
will eventually run into a party that uses a bank that still uses MICR readers and it will turn into a massive headache. But it's misleading to imply that MICR is a security feature, it wasn't even used until the very late '50s.
The security model of checks is complicated. Ultimately the paper document is not really regarded as any kind of authentication, it's usually destroyed fairly early in processing (by the depositor's bank) and replaced by an image. In some cases, less common today, it may later go from image back to a "replacement document" which is a brand new copy of the check produced for convenience when clearing with a bank that doesn't yet support clearing by image. Nothing about the document itself is important to or required for clearing, only the data on it.
Yet it is common for printed checks to contain various anti-counterfeiting features. From first principles this seems a bit confusing.
But checks are not authenticated by their own right. A party who accepts a check is taking on a certain amount of risk, the amount of which depends on the nature of the situation. They are not really "authenticating the check" but actually performing a risk analysis, in which only one of the factors is security features present on the physical document. When you ask to cash a check at a grocery store, they are unlikely to cash it unless it is a payroll check from a nearby company and has expected security features---this is because they are taking on a relatively great risk. But when you deposit a check via ATM, you're often credited the full amount (up to some limit) instantly with virtually no verification besides the ATM trying to parse the number. This is because, as a holder of an ATM card, you have an ongoing relationship with the bank and they feel fairly confident that, if the check is bad, they can recover the value from you in some way.
My point is that talking about forging checks for payroll direct deposit reasons is kind of the most extreme possible case. The only reason you're asked to present a check is because most companies have had way too many incidents of people providing the wrong routing and account numbers and it turning into a real headache when their paycheck disappears. If you went to the trouble of forging a check in order to set up DD, I suspect it's also very likely that you got the routing and account numbers right, clearly you put some effort into this. So in practice a "forged" check is probably every bit as good for their purposes as a legitimate one.