rds21

Hi All, Apologies in advance if this is a long post, however I want to give you all the details before you give me your opinion. I have a 2015 Crosstrek with 30,000 miles on it, and I'm trying to somewhat keep up with the maintenance recommendations so I had the front & rear differential fluids changed at a local shop. I did recently have the oil changed at the dealership, but the 30k service package was $800+ & 4 hours (had to pass). Here we are 15 days later I went on my first "trip" for the holidays (200 miles each way) and the AT OIL TEMP light comes on an hour into the drive! I pull over per the manual, idle until it cools/light out....every 45 minutes. At one of the stops I notice the coolant reservoir is basically empty and purchase the best 50/50 mix possible just to get it to the MIN line as I want to only use Subaru super blue coolant, but I won't be able to get that for a few days. Made it to the in-laws just fine and convinced myself it was all due to the low coolant. An hour into my trip back home BAM, AT OIL TEMP is back. First stop I let it idle and cool but it SMELLS HOT. This is my first new car; previously I had a 1999 supercharged Buick regal GS and I haven't smelled this smell since I had that 16 year old car going on a 100 degree day. Unfortunately it was only 20 degrees in Chicago when this happened another 4 times. Researching a bit more it's apparent that my engine light is related to transmission fluid temperature. The people at the local shop did mention they had issues filling because the fluid was thick and they didn't have a gravity pump, and now I'm connecting the dots. I'm assuming they did not completely fill the differentials and the first decent trip I took got the fluid warm & low enough to strain the transmission??? Is there any serious damage that could have occurred? Should I have any other fluids changed/parts inspected since I suspect very high heat built up somewhere? How hard do I need to crush this local shop? I was so excited to have a Subaru and want to nip this in the butt while it's under warranty and really appreciate any input you have.