I raised this issue over on the bug tracker, hoping it would be an easy, "common sense" fix by devs. https://github.com/OpenTTD/OpenTTD/issues/6799
So I'll raise it here to generate some awareness and discussion.
Since TTDPatch there have been graphics in the base graphics set for separate sprites for road vehicle and tram stops, but these graphics were never implemented. Instead both use the same set of sprites, and this carried over into OpenTTD.
There should be a way for NewGRF road vehicle sets and tram sets to implement independent graphics for one that do not affect the other.
Frosh raised this issue:
The reason is simple: Which sprites to use for shared bus/tram stations?
My answer for this: which ever one was initially built. If you build a RV station, and later run a tram through it, all you're doing is adding tram tracks and catenary. If you build a tram station and later run a road through it, you're just adding the road surface. You don't need to update the graphics to reflect that. If the player wants the tram stop instead of the RV stop, they can overbuild on it with the appropriate tool.
It would be nice if you could somehow have a third option for a combined RV/tram stop, with a player deciding between the three options, but it's not necessary and I don't even know how feasible that is. I'll be satisfied if you can just have separate graphics.