I talked about 6.35 because you said it wasn't supposed to work whereas it is working and the behavior is consistent since at least that version, but probably since the feature exists.
I'm not entirely sure that just because the behaviour hasn't changed in N years that it should work. By your logic, the fact that $input() does what it does now means that it can't be a bug, since it's been that way for so long. I certainly don't believe that's true, and I doubt you do too-- my point is that it's just as plausible that u was never really meant to work properly with dialog windows. Khaled would know better.
I guess the question is this: is using the 'u' switch *really* the recommended way to make a modal dialog with $input? The behaviour of "use the current active window as the parent window" doesn't really sound like that's what it is for.. so while you may have been getting the behaviour you want, it might have just been a side-effect, not a feature. In fact, the fact that u makes the dialog modal might be a bug in itself. There's no equivalent way to make an $input modeless in a non-dialog scenario (//echo -a $input(x) from a channel/status window is modal, same with the u switch), so maybe this was never intentional.
Maybe Khaled can answer the above question (how an $input can be declared modal in a dialog)-- I think that would clarify things.
