So I'm working on a 1.12 pack using tool progression (stating the obvious), and I just thought I'd share my findings of misbehaving blocks and tools.
All picks and drills seem to work perfectly, or I guess were already at the level I wanted... Except the Actually Additions Drill. It seems to be stuck at pickaxe=4 and won't change. It's also the only item on my list with metadata. It can be dyed so the meta is 0-15. The listing for it had no meta. I tried :3, 3, and ., then gave up. I wanted it at pickaxe=5 so it's fine, just weak.

Block Exchanger tools and wands all bypass mining levels and swap anything. Cyclic's wands have a block blacklist in configs which works. Building gadgets does as well... but it doesn't work, at least not for the exchanging tool. Not Enough Wands' swapping wand is also unstoppable. I made restrictive recipes for them in Crafttweaker obviously.

Block Breakers are annoying as you know. I saw three distinct types of behaviour...

Break everything: AA's 3 block breakers, Industrial Foregoing's, Super Factory Manager's block gate, Integrated Tunnels' world block importer, Mek's digital miner, RF Tools builder with quarry card.

Break only hand breakable blocks: Open Blocks', EU2's mech miner, Cyclic's block miner

Breaks properly as set in tool overwrites (the good bois): Random Things', mana spreaders with bore lens, and of course machines that mine using a pickaxe you give them.

Update and corrections:

Building gadgets kindly fixed their blacklist feature, not that that's important for your end.

As for the "Breaks only hand breakable blocks": ... I'm an idiot. They mine based on the mining level of the diamond pick, which I had "disabled" by setting to -1. Those breakers are actually the most compatible with tool progression.