Okay, here are some findings, on the 1024x600 netbook, Win7 Ultimate, task bar set to auto-hide.
version 3.4.7218 P
version 3.3.7165 P as reference
Unlike Freddy, I don't see new scroll bars on any Preferences panes, or Plugin config pages. It looks like the only difference from the previous version I can see is the odd behaviour of the Layout(1) scroll bar. I note he's using Win 10, and I'm using Win 7; is it a differnece in window handling between those versions...?
Opening Preferences, and selecting Layout(1), the scroll bar on the right starts as a standard Windows scroll bar, with a button at the top (the bottom is off the screen), normal Windows scrollbar width, full height of the window; it won't scroll at all. Switching to another preferences page and back to Layout(1), the scroll bar loses the button, and becomes the narrow 'MB' scroll bar width, filling only a fraction of the screen, which allows the pane to be scrolled. I can get as far as 'progress bar on bottom', but no further. The bottom section of the pane, that contains the buttons on a bigger viewport, and the pane border, are off the bottom of the screen.
Selecting 'Arrange Panels', the 'MusicBee Panels Configuration' pane opens with a scroll bar on the left. The scroll bar allows me to get to all the control elements. The pane is small enough that all three Apply/Save/Close buttons appear.
The Preferences 'Save' and 'Close' buttons 'float' over the preference options, just above the bottom of the screen (the button text seems to sit exactly on the bottom line of the screen), on any panes where the full pane cannot be shown (except see below...). The 'Apply' button does not appear at all on these panes.
On the 'Views Configuration' pane for the Main Panel/files Panel Settings/Show Settings button, none of the Apply/Save/Cancel buttons appear, and the scroll bar doesn't reach them; it looks like the 'click to set overrides for the configured MusicBee layout' section is reserving space in the pane, which forces the Apply/Save/Close buttons off the bottom of the screen.
On my larger viewport device, the Preference pane is a fixed size, and each of the sections fits within that pane. The buttons at the bottom are in a fixed position. When deployed on a smaller viewport device, it's not possible to get to the bottom of this fixed size pane; it's off the bottom of the screen. What I think is needed is the ability to scroll the entire contents of the preferences pane, section selection panel and all, within the available viewport dimensions. This would require enquiring from Windows the available viewport dimensions, and sizing the Preferences pane to suit, applying a whole pane scrolling if required. Apologies if that's what you were already trying to achieve...