Major thumbs up for doing this!
I didn't yet test all of the new changes, I only did some small tweaks to a tune using the new version, but there was one problem (which I already had with 2.3D, and might not necessarily be a PT bug anyway since this is a somewhat tweaked Workbench (ClassicWB on an Amiga 1200)):
I multitask with PT by pressing the key above tab to switch back to Workbench. Whenever I return to PT by clicking the topright button in WB to switch screens, mouse clicks aren't handled properly in PT. All clicks in PT seem to get processed by BOTH ProTracker and Workbench, in that order, and since the mouse cursor is still located on top of the "screen switch" button in Workbench, this means that every left click inside PT now switches me back to Workbench. Keyboard works fine though. Anyway, I would love to have a fix for that, if possible!