I am trying to create a column in a table that\'s a foreign key, but in MySQL that\'s more difficult than it should be. It would require me to go back and make certain changes
Enabling these constraints in MySQL takes almost zero time. If they save you from even a single bug due to faulty PHP or other code, isn't that worth it?
Keep in mind that the sorts of bugs you'll save yourself from can be rather nasty. Finding and fixing the bug itself may not be hard; the nasty part is that once you've fixed the bug you'll be left with a bunch of faulty data that may not even be salvageable.
I wouldn't even approach this problem from the "well, something other than PHP might access your data someday" angle. That's true, but even more important in my mind are the the headaches, time (money) and data loss that you can save yourself simply by adding a few simple constraints.