Ok, unlike Gladius I actually did some testing instead of just mumbling about "
similar hidden bonuses for various reasons" without sharing any. Great help chap!
Today I decided to delve into some of the console commands for more accurate testing.
The modification of the negative vampire stage effects (15/30/45/60 stat reduction), DESPITE it not showing up in the active spell list, got me thinking...
Turns out, the +100% frost resistance does go up to
+125% afterall, as well as the fire resist to
-125%. (player.getav fireresist)
This leads me to believe that all effects that are innately yours will get modified. Same goes for High Elf's racial spell which adds 10 times magicka regeneration. Before it was kinda hard to test without console commands as you can imagine. But now the concrete numbers I got are as followed:
player.getav MagickaRate: 3 (probably referring to the 3% of maximum each second outside combat)
With Highborn powerer it becomes:
34.25After removing my vampire undead status:
28.00I also tested with adding/removing the Apprentice stone (100% regen) and removed my Recovery perks in restoration which adds 50% regen. None of them have any influence on the number you got from the console command I used. Clearly the highborn power is modified not only by a 50% duration but also by a 25% magnitude.
I assume (feel free to test) that the same applies to the Histskin and Adrenaline Rush powers as well. But more interestingly would be to test the Orc's Berserker Rage power. +25% of 50% extra damage and damage reduction should result in another +12.5% bonus PLUS 30 extra seconds of wtf-pardon-my-french-ness.
Now the main thing I wanted to test was whether or not the illusion and sneak 25% modifiers also get boosted by another 25%. However the commands
player.getav illusion / illusionmod / illusionpowermod and
illusionskilladvance (the only 4 related to illusion I could find) don't seem to give me any useful info regarding this matter. If someone has any idea's on how to test this I'd love to hear about it. I guess one option would be to find an NPC at the limit of your illusion spells and then add the Necromage perk to see if the extra +6.25 (25% of 25%) makes a difference. But that technique seems a bit unprofessional.

My assumption however is that it DOES get increased. After all, what difference is there with +25% sneak/illusion and +100% frost resist or -60 stats. They're all vampire bonuses and the latter ones do get modified by the Necromage perk.