Most of those questions are aesthetic and largely personal. You may not be able to match the muntin size or style exactly, but the naked eye is easily fooled. Whatever you decide to go with, make it something that you will happily put in the rest of the home when you are done. If you haven't tried Ultra Windows in Houston, I would give Randy a holler there.

Not likely a wood chip. Possible that it picked up a pebble and flung it when they were grinding it up. That picture is terrible and if they are facing inside, it appears the damage was done from the interior to be honest. With regards to your other questions: Totally depends on the window in question. Usually glass is measured and prepared before coming to the jobsite to deglaze and repair. Find some of the operable units and look for warranty/serial number on the glass, in the head jamb, on the sashes, etc. If they have acknowledged that it was then that damaged the glass, they will probably bill you and do some sort of warranty holdback credit on the open bill for a modest amount. Without seeing the window, I couldn't even hazard a guess as to the repair/replacement cost so that holdback would be dependent on that.

IGUs (Insulated glass units) are replaced as a unit and can't be field repaired on one side. Can the window sash be easily removed from the window? If so take it to a glass shop and get an estimate on the repair. If the frame comes off easily then one can take just the IGU to a shop and have it replaced, then reinstall in the frame. I can see three options: 1) have the tree guy coordinate the reapir with your tenant, 2) Call a local glass company, have them go to the property amd do the repair and deduct it from the tree guy's invoice. 3) Ask your tenant to handle the repair and compensate him/her accordingly. You don't say the size of the window and you're picture doesn't hint at the level of effort to remove and replace the IGU on this particular window, so it's difficult to guestimate the level of effort to fix it.

Thanks @todd!! Hopefully the heat buildup won't be an issue. I called up Provia (such nice people) and after describing my set-up and the lack of direct sun, they said it shouldn't be an problem. For issue 2, the window that came was smaller than the exterior rough opening, which leads me to believe it could/should have been bigger. My general contractor had already framed the walls using the original windows as guides, so this smaller window throws everything off. Anyway, they are in now. Have you ever saw drywall put in at an angle, where I'd start it where the wall framing is and angle inward to meet the window frame, or is that a ridiculous thought? The caulking you use sounds more sensible. Alas, that ugly, gloppy white caulking with whatever crap blew by in the wind and stuck to it is in, so I guess I'm going to have to live with it. And the softness of the pine, oh if i knew this, I might have made different choices. The guys filled the gouges with putty, but of course you can still see them. Brand new windows and they are already looking cruddy. What a bummer this all is.