I think research fit is SO important for your MD-PhD & is what drove my lists in the first place. Like this is the reason why MD admissions is diff to md/phd. If the leading PI in your field is at Penn, IMO that's what will shape and drive the rest of your career. Your scientific 'family' is more important than anything else as that will influence your papers, grants, future direction/lab, etc. If you think you can do your PhD in their lab, you should go for it.
Feel free to DM me privately - I have a friend in the Penn MSTP program who had a very similar situation (and same choice dillema actually lol) going in with having an awesome lab fit, and as a result she was able to start her PhD work much earlier, and is slated to defend with only 3 years of the PhD and because she hit the ground running also got some of the most prestigous grad awards/grants which is such a huge thing if you want to become an investigator.
You'll also be spending 7-8 years there and Penn's area is still very chill, with still having a lot more to do than New Haven which will def get old after a while, as well as easier more direct flight/travel to West Coast. It's also very close to so much nature right in the city (wissahickon valley park, fairmont park, and just as close as new haven if not better to hikes, national parks, and state forests) so I wouldn't count Philly out in that aspect.
Curriculum wise, although the Yale system is awesome, I'm not sure if that a few extra requirements is more important than having your prime pick over the top MSTP in the country, location, and research fit especially since that will be training you and helping you retain more longer as you take the break from med school in your PhD (which imo is also why the MSTP is so well regarded & has better outcomes - there is also an oddly high amount of YSM MSTP students doing 9+ years if you look on their website). Lastly, I know a few MSTP students at YSM and also the buddy from my interview day and I discussed, but on the contrary, there isn't as much unified-ness as a direct result con of the Yale System. I think this is definitely something that may vary but just a note to think about since you listed it!
Additionally, Penn is a much more diverse city (in all aspects of the word - which is very important IMO for research, medicine, and personal life) and with so many more hospitals, you're clinical training is going to be much better which is one of the biggest cons I hear about Yale.
Overall you can't go wrong, but I think that's why Penn is the safer choice - good luck and congrats!!!