Outdated and premium are two different things. The Model X costs more and therefore has more "premium" features.
Don't get me wrong, I love the Model X (owner for 2.5 years), but it needs an update. If you need a third row, definitely get the Model X. If not, the Model Y is a great option. Here is my rationale -
Model Y Newer Tech/Innovation - Updated battery pack (2170), more efficient 121 MPGe vs. 90 MPGe (20" Perfs), 250kw Supercharging, heat pump (this is big for northern states/colder climates), Model Y has more leg room in front and rear than MX, updated interior/landscape screen format.
Some of the items you brought up:
Homelink - non issue, just pay the money to get homelink.
2nd Row Seats - I have a Model X 6-seat and the 2nd row seats are not especially comfortable. Many people have complained they are too narrow. Less leg room than Y.
Automatic Doors - This is not a straight win for the Model X, as they are not very practical. I rarely use the presenting doors feature on the car since the doors open when I don't want them to. I also don't always use the automatic close door feature as the door tends to slam hard. That leaves the FWDs. They are great for getting in the third row and putting kids in the 2nd row. However, they are extremely showy (to the point where it is embarrassing). If you park this car in a public place and open the FWD doors, I find that someone comes up or makes a comment at least 50% of the time.
Bioweapon DM - I have used the feature a handful of times in the last 2.5 years. Usually to get rid of a bad smell. Gimmick.
Stereo - Where is this coming from? I have spent significant time in a Model 3 Perf and the stereo sounds better than my premium stereo in my Model X. Many say the Model 3 stereo is better than S and X. My guess is that the M3 stereo is a transplant into the Y.
Have you driven the Y? I spent an hour in each vehicle back to back and I've driven every variant of the X and 3 a dozen times over the years. I sat in every seat and played with every setting and switch they had. I know that can't match your 2.5 years of ownership, but I've test driven and owned enough vehicles in my life that I can get a feel for a car very quickly. After spending time in both, I did not come to the conclusion the Y was superior tech and the X needed to be taken out behind the woodshed and shot. The Y is not a step forward for me, it's a stripped down cheaper alternative to get the masses into a Tesla. And they did an outstanding job.
Heat Pump - I live in the south so I guess I really don't care about it or the extra noise it brings. But, I don't see that as a major tech advancement.
Touchscreen - I find the landscape touchscreen a step back. Widescreen is great for watching movies and playing video games, but these are two things I'll rarely do if ever because when I'm in a vehicle I'm usually driving it. I find having it in portrait more useful since I don't have to reach over as far and can have the rearview camera on at the same time. The binnacle makes it all that much better. I don't know where this widescreen is better came from anyway. Most of us use our cell phones and tablets in portrait mode a majority of the time for a reason.
Stereo - The stereo in the X was better...period. I played the same songs adjusting settings to where each sounded its best and there was no question to me the X had fuller sound with better highs, mids, and lows. I'm not saying I have golden ears, but I've spent obscene amounts on audiophile equipment chasing that extra 1% in sound (I'm far less critical now in my 40's which is why I haven't gone near Head-Fi in years and on top of that, I really don't care anyway).
Interior/Seats - As far as legroom, the two were very close and I felt more comfortable in the X as did my wife. Maybe the pano windshield and extra width made it feel that way. I didn't spend much time in the backseat of the Y because it was uncomfortable, but I didn't get any feeling one was more spacious over the other. Specs on paper don't always translate into real life. Overall, I don't find the interior more updated in the Y. It's just more spartan.
Charging - Yes, it will get done charging faster in my garage overnight as I sleep. Yes, the person in the Y will get done charging faster than me on the rare occasion I use a supercharger.
I'm not trying to disparage the Y, I reserved the AWD back in October because I was hoping it would give me most of the utility of an X and also that Tesla performance for $30k less, and it basically does. The X just serves up all the features I expect a vehicle to have in 2020 while the Y is missing a lot of them. When I buy a new vehicle I try to move the ball forward. Charging speed and heat pumps aren't the tech I'm looking for.
If someone told me the X was the successor to the Y, it would seem completely plausible to me. But, just like a modern day Honda may have better tech than a BMW from 10 years ago, it doesn't mean it's a better vehicle (I own both so I can judge).
Enjoy your X!