For games that doesn't support Steam Cloud for saves etc., or in general moving files over to the Steam Deck from your PC, I highly recommend setting up Syncthing.
It's available on the Discover store in desktop mode and can be set up to run as a service to ensure that it's always running on Steam Deck, if you're so inclined. There's a myriad of guides out there if you search around, should you need help setting it up.
OVPN still seems to support port forwarding, though it's worth pointing out they were recently acquired by Pango.
Oh and the carrying/storage case it comes with seems to be different for the 512GB version. Not sure about the 256GB version though.
Does the eMMC version allow installing an NVMe drive?
Yes, the only hardware difference between the different version is really only the screen and the drive it comes with. You can technically buy the 64GB version and replace the screen with an anti-glare one at a later date, as it can be bought as a spare part for not much.
Personally I got the 64GB some time ago and am still happy enough with just an SD-card with good speed and decent size. I suspect that will change down the line, but right now I'm happy.
It's the second time it's been discounted so far. The first time was on March 23rd this year, on Steam Deck's first birthday.
For what it's worth, the game works perfectly out of the box on Steam Deck via Proton, didn't even had to force compatibility to use any specific Proton version. So at least it does work, and you can see others being successful on protondb too as linked by @PeachMan.
LibRedirect is a great way to access a wealth of sites like youtube, twitter, reddit, wikipedia, etc. via alternative privacy friendly frontends instead of directly.
While not an inherent guarantee of privacy, nothing really is, it makes the process of rotating randomly between these frontend instances for each visit a breeze, and easy to hop to a random new instance if the current one is down/not working as expected.
The only real issue I've stumbled upon were random crashes, which crashes the whole Steam Deck oddly enough. Since changing to Proton Experimental I have had such crashes maybe once or twice in ~20 hours, so I would say that mitigated it.
800x500 is a great resolution to play at, I find. Every text is perfectly readable and HUD is at a great size, in fact, it feels like it's made for Steam Deck. Also changing to 32-bit color mode is a good idea.
The most important part really is the controller layout. There are some great community ones out there, though I found myself customizing it a lot to fit my personal taste.
To be frank, I haven't played further than playing through Liberty Island on GOTY, and a bit further. Personally I opted for Revision instead, with vanilla map type, vanilla soundtrack, all HDTP models to false, New Vision disabled, and normal Revision gameplay style (which brings a lot of QoL stuff, bugfixes, but nothing I've found to be really intrusive).
Revision on Steam Deck, with the changes I mentioned, is very stable and faithful enough experience in my mind. The only problem I found was that all data vault images are still for the Revision maps, so they won't line up and will quickly become confusing. I ended up manually swapping the images, which was a painstaking endeavor I wouldn't wish on anyone, but it worked out in the end. Might end up uploading it somewhere at some point, but I should instead really just report it to the team and hope it gets fixed. My main reasoning for choosing Revision was honestly the achievements, it's a fun bonus and a ton of them still apply to vanilla maps. That, and the fact that it just feels like integrates seamlessly into Steam, being a mod with its own store page. And once I'm done with this, I'm very tempted to just jump back in and play through actual Revision with Lay D Denton.
Though if I started out now, I would probably seriously consider taking a look at Transcended or Deus Ex Randomizer with Zero Rando mode (just heard of the latter first here, so I'd have to look into it more before choosing). I'm not sure how smooth the process of getting that into GOTY on Steam Deck is, and I'd miss out on those achievements from Revision of course, but it could be well worth it still.
That all said, just playing GOTY straight out of the box works, with the few things in mind which I wrote about above. There's a myriad of bugs and stuff in GOTY that are just there, of course, but it's not related to Steam Deck and still play very well.
Same here. Countless time. Doing my full complete playthrough right now thanks to the Steam Deck and just about to finally finish it! Definitely thinking about trying this randomizer afterwards.
Quote from Valve Hardware Warranty.
In other words, simply changing SSD doesn't void warranty, but damaging the Steam Deck in the process of doing so does.