The other overage sources were: plumbing (most of the lines had to be replaced), roof/siding (we used a high quality company and paid for it), drywall (we decided mid-project to raise the ceilings in 2 rooms) and “misc carpentry/trim” ( all the extra time we paid his crew members given we expanded the scope).One of the more unnecessary (ok, dumb) things I did was pay his crew hourly.

My largest renovation, which was NOT a gut flip, but had some foundation issues, did NOT need hvac work, or a new electrical service, or new plumbing, and I did a bunch of the work myself (cabinets, trim, paint, tile...) comes out to $63/SF.

We just framed them in with 2x4s and trimmed them out.

Replacing all trim 4.

It's like saying don't buy a hedge clippers to trim your yard because in a few years you'll be able to 3d print one at your house.

Test strip on the right is from the inside trim on a kitchen window I tested last month.

First, if the plumbing work required a permit, I wouldn't hire an unlicensed plumber, as they wouldn't be able to pull a permit (and I'll never try to get around pulling permits, as that's a liability risk I don't want to take)...But, if we're talking about work that doesn't need to be permitted -- for example, replacing a trim kit on a faucet, replacing a toilet, etc. -- I'm happy to hire a handyman or a "plumber" who isn't licensed and/or isn't insured. 

If the answer to question 2 is no, trim it.

This involved a serious water-main replacement and all new everything (except the roof and walls), even serious tree-trimming done by experts.

Trim in and punch out should be done before final payment.