To answer your clan question, yes, you can have it so the building price increases per toolcupboard owner with the Hourly cost per authorized player property. If set to 10 for example a solo will cost 10 per hour while a clan of 8 will cost 80 per hour (on top of other costs)
To answer your building issue, I'm not sure exactly how those plugins you listed work, but I do know that Raid Protection only updates the floors if they were naturally placed. If a plugin places the floor for you, or auto upgrades it, it may not refresh the counter as the hook for a player building a structure isn't triggered. That being said, if you eventually naturally place or destroy a floor (or any other building block) it should retroactively update as well. Which is why it is correctly updating when you replace the toolcupboard. I can double check this is working for you later today.