Thank you for bringing up this unresolved topic! I’ve been watching the topic of indoor mapping for years, but the current lack of a consistent way of tagging makes it less attractive for both mappers and developers than it should be. And you have already addressed the most critical obstacles in your post.
However, to emulate the success of Simple3DBuildings, I believe that the tagging schema would also have to be simple. This was an important goal at the meeting where we laid the foundations of 3D tagging, and to me, this means use relations as little as possible. For 3D tagging, at most one relation per building is being used, and even that is optional in practice. All the big renderers have no problems with relation-less buildings and most 3D mappers don’t use the relation.
When I look at the IndoorOSM proposal, I get the impression that simplicity was not a design goal. The most obvious example is the use of OSM IDs in values which you have highlighted already. However, there is some other factor that makes things unnecessarily complex (as already pointed out when IndoorOSM was originally proposed): The relations are not really necessary in most cases.
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The tags describing the entire building can - and should, for backwards compatibility - be on the building outline.
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Whether an element is within the building would almost always be clear from being contained within the building outline.
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What level a feature is on could be defined by a level tag, rather than the membership in a level relation.
So I’m strongly in favour of making the relations optional. With this convention, the “POI only” tagging with level tags on the POI would not be a special case, but simply a normal application of the tagging scheme.