|King of Vrock|
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As a GM with a group that fluctuates between 4 and 7 and one whose run several campaigns to 15+ in 3.5 and PF, both Epic and currently Mythic I understand your frustrations. That being said as a GM who also works full time you're going to have to learn you aren't exactly beholden to the RAW. You can and should break them now and again to adequately challenge your group. Now I'll make some assumptions seeing as you have a laundry list of houserules, that your players are experienced with not only the rules, but with playing with each other. Nothing wrong with that at all, but it does mean the core assumption (15 pt buy, 4 player, 4-5 APL encounters per day) isn't going to be a good fit for your table.
So here are just a few tips I use to challenge my group. In a given encoutner for every factor of point buy above 15 I add +1 CR. For groups of 6 or 7 I also add +1 CR. Larger groups also face 50% more minions and Named NPCs with max hp. Past 10th level I add double max hp to named NPCs and max hp for minions. I use the Advanced simple template liberally.
High level play is an area where few groups regularly congregate so there has not been the rules guidance or support from either Paizo or 3PPs (that I know of) that specifically address High Level encounter design. The abilities you mention like nondetection/mind blank, access to teleportation, flight, scrying are things that you not only have to be mindful of... you have to actively include them as assumptions in your encounter design. Make it so your players have to teleport several times in order to even come face to face with the villain. This game is all about resource management so you have to force them to drain power. If you can use more encoutners per day, 5-6 is a better number. Don't allow them the 15 minute adventuring day. Force them to continue moving when low on resources.
BBEGs should have defenses against common high level tactics because villains shouldn't be stupid. As PCs get more powerful their abilities should become more common knowledge and you can use your GM metagame knowledge to gameplan for your group's common tactics and abilities. Now I'm not saying to constantly use this to ignore your players strengths and/or exploit their weaknesses, but do so in key moments of the story. No one enjoys having the main villain one-shotted before they can act.
Limiting buffs is a common houserule, one I know my players would object to. But it does take some of the math out of Mathfinder! My players routinely forget bonuses they have up, so limiting them make it easier on both sides of the screen. Don't make it too complex. You can handwave the school interactions as "that's just how the magic works."
--Vrock & Awe