I don’t feel like it’s a substantial issue. If I’m thinking like that I’d have an issue with the idea that his X-wing even works at all being dumped underwater like that for years.
Honestly, I don’t think anything we’d do to TLJ or TROS would really reconcile things anyway. Door panel aside, the plot of TLJ itself implies that Luke could not have flown his fighter, otherwise he would have to Crait. (Logistics or travel time be damned; Star Wars has always moved at the speed of plot.) This story necessity, moreso than the door, poses the incongruity.
I mean, this is a universe with plasma blades and a magic system that only shows up in people with a high amount of fictional organisms in each of their respective cells.
Also, the First Order would’ve shot Luke down if he actually showed up on Crait.
Well I always undererstood it the exact opposite way: that the reason Rian showed the ship in the water shot is so that you wouldn’t suspect something was up with Luke in the climax.
I mean, his appearance matches when he was the legend, he’s holding the Skywalker saber, and he leaves no footprints at all.