Automating the 'Atomic Reconstructor' (and any other item drop crafting mechanics) is really annoying when wearing a magnet. Demagnetize is a very lightweight mod to block magnets in an area.

Automating the 'Atomic Reconstructor' (and any other item drop crafting mechanics)

This might get fixed by simply adding Modular Machine equivalents for all mechanics that normally need item drops. There's already an unofficial implementation of it.

I'm pretty sure Draconic Evolution has a block which disables magnets in a area

I assume you are referring to the 'Dislocation Normalization Field Projector'. That seems to only work with the DE magnet, and is also semi-late game, since it requires draconium (I'm not quite there yet). Perhaps as an alternative to adding the 'Demagnetize' mod, the recipes for the DE magnet and the Dislocation block could be tweaked to be more easily obtained.

The atomic reconstructor is really the only item with block drop mechanics for crafting, and the thermal magnet has a black list option so items are not picked up by it. Another option is simply hiding the recontructor behind some blocks such as glass or other blocks, so that the magnet will not attempt to pull them.

Item Dislocators from DE also have a block that disables dislocation within a certain range. Between that and magnet filter settings, I don't have any issues with AR stuff getting yanked into my inventory.