TAStudio doesn't inhernet the Windows that need to be displayed on top when "Always On Top" is in use.

[Spikestuff]

Bit of a hard explain, basically the Always On Top setting affects the other smaller menus that disable moving the TAStudio window.
In comparison to BizHawk itself where these Setting menus that suspend Hawk would appear above them instead.

[YoshiRulz]

I think you mean that the flag isn't set on child dialogs? Which should be easy enough to do, but I don't know whether we should since I'm not familiar with what the convention is on Windows. (edit: It may also be that they're not getting parent: this set, and doing so would automatically fix the keep-above behaviour like I'm describing below.)
On Linux, modal dialogs done "correctly" (Wayland and/or KDE lib call) have an independent flag, but when it's false they inherit the keep-above behaviour of their parent. Otherwise you're expected to unpin the parent window or move the child into view since those are core DE features.