MacBook – use Shift, Alt and Control Modifier Keys Together With the Function Keys on the Touch Bar

I've configured my touch bar to always show function keys in one program where I use those frequently (IntelliJ IDEA, code editor). Many hotkeys in IDEA are triggered using a function key together with shift, alt or control, e.g. for renaming a variable, I use Shift+F6.

With the emulated function keys, this does not work, the program acts as if I had just hit F6 without holding down the alt key.

It was no problem with the hardware function keys on my old MacBook.

Is this a known bug, or a limitation one has to live with? Or is there some way to work around it? Perhaps I'm just to stupid and missing something obvious?

This is a major pain for me as a software developer…