As the author of the commit you want to revert, I'll explain the rationale: when there are many buttons, without scrollbars, it's even uglier than what you show. It can even be completely unusable, if the window is higher than screen resolution. Those scrollbars are here for a good reason.
Of course the behavior can certainly be improved, for example using more than 2 rows, or by not showing scrollbars at all when there are not enough buttons. But simply reverting the change is not improving anything. It will reinstate a bug that was worse than just cosmetic and was already fixed years ago. It's simply not constructive.

when there are many buttons, without scrollbars, it's even uglier than what you show

How can it be worse (unless the window is higher than the screen)?

It can even be completely unusable, if the window is higher than screen resolution.

I expect that in almost all cases the window fits on the screen. Using the proportions of this screenshot (45 px per row and 300 px for the rest, including decorations), 30 axes+buttons fit on a 1000p screen. If a window does overflow, it can still be panned to access the hidden areas. (In Plasma, with Alt+mouse drag.)

But simply reverting the change is not improving anything.

I think that qjoypad is better without that change, not only for me but also in general. If the issue of the overflowing window has to be fixed, it should be fixed without sacrificing the look in the common case.

I expect that in almost all cases the window fits on the screen. Using the proportions of this screenshot (45 px per row and 300 px for the rest, including decorations), 30 axes+buttons fit on a 1000p screen.

Just as an example, my system detects one of my joypads improperly, with too many buttons. Without the scrollbars, here's what it looks like (real joypad):

If a window does overflow, it can still be panned to access the hidden areas. (In Plasma, with Alt+mouse drag.)

You're overly optimistic, only a very very small fraction of users know this shortcut. And if the window is too high, it's clearly a UI problem, the app should be fixed.

I think that qjoypad is better without that change, not only for me but also in general. If the issue of the overflowing window has to be fixed, it should be fixed without sacrificing the look in the common case.

You could remove the scrollbars AND replace them with another fix. But you don't fix it at all, so you just add a bug.