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.