Yeah, it's not great. But warnings are technically not errors. So you don't HAVE to follow them - the software doesn't always know.

By the way, most crossing warnings can be fixed - these are more like "upgrades". The crossing tagging scheme was standardized not too long ago and most crossings are using the older imprecise style. You shouldn't bulk update them, but if you are updating the area, then feel free to upgrade them.

Just a side note - other editors like JOSM or many validation tools (you can toggle some on in the editor data layers) will show a LOT more warnings, errors, hints, etc. There are so many no one will ever be able to fix it all, so it's just something we have to live with. This isn't even mentioning that mappers don't actually agree on how many things should be drawn or tagged, even for what seems like basic significant features.