"allow you to drop down to make lower level tweaks as you would on 'bare metal' NPM"

Meteor is entirely open-source and I've had no trouble diving into the lower levels to accomplish what I need to accomplish. Everything is split into reasonable packages and is relatively easy to traverse.

If anything, the Meteor team hasn't done a good enough job showing their true value (realtime via oplog->client updates, etc). Most of the current controversy stems from front-end developers jumping on the React bandwagon, splitting up the community as it stands. Not a big deal IMO.