Recently while playing with the digital miner, I had the idea that, for removing caves and such, it could replace air (practically used with stone). This would allow easier building of large underground factories without manually clogging up said caves

I don't think it should be done with Digital Miner. Buildcraft already has a Filler, what exactly can do what you expect. As digital miner works without checking it's environment (it's placed on floating island or just over a cave), replacing air should cause problems.

Obviously it could be a config, and it could only work on air adjacent to stone. Also, just because another mod has a feature, does not mean another mod can not have something like it. My reasoning is that because it can remove ores and replace them with another block, but only if said block is available in it's inventory, would it not make sense for it to spot patch said holes, as well as remove caverns that would impair underground base building.

Nah, I don't think so. The Digital Miner already serves too much as a "Digital Builder," I think this would just make it worse. Thanks for the suggestion though!

Okay, I guess I'll add it to Thermal Tinkerer EVENTUALLY (as a feature of the Laser Ore Leecher)