Thank you for your report, and apologies for not having been able to look into this earlier.
First of all, I am unable to look into this using the Bridgewater-Brunel server game owing to my computer issues at present. However, I infer that the issue is probably one relating to the system for determining whether crossings may be built and the consequences of this. Access rights permits the construction of crossings. Once built, each independent way on the crossing has its own independent set of permissions based on the owner of that way. That is quite fundamental to how the game works. Thus, any removal or alteration of the road part of a road/rail crossing will need the permission of the owner of the road. The rail can be removed from over it by the owner of the railway.
There is no easy way to do anything more sophisticated along the lines of some of what has been suggested (such as special treatment of mixed owner road/rail crossings as to public rights of way, or different treatment according to which was built first) without some fairly significant redesign of the underlying system for ownership rights, which, given current constraints on coding time, is unlikely to be an efficient use of that time to address an issue of this nature which arises in relatively limited circumstances.
One thing that might be worth considering, however, is whether to permit road/rail crossings to be built on the basis of access rights alone, or whether a crossing between two types of way should be able to be built only by the public player or the owner of the existing way already on the land. Even this would require some substantial extra coding, as there is currently no code differentiating permissions for two roads joining each other and a road crossing a railway (etc.).
I should be grateful for people's views on this somewhat complex question.