Found a solution. For anyone else wondering, the level caps are stored in the TorannMagic.dll (choose the version that's the same as you game version). Open it with dnSpy, find MagicPowerSkill (by pressing ctrl+shift+k and searching levelmax). There you will see things like this.levelMax = 50 below a bunch of labels - that is what you are looking for. To take mana pool as an example. "TM_global_spirit_pwr" is the mana pool and below it there is "this.levelMax = 50;" which limits the max amount of points that you can invest into this ability. Simply increase this number and the limit will be increased as well. You may attempt to do it by right clicking on the value and picking "Edit Method", but I wasn't lucky with this as the app always throws a bunch of errors at me. So the workaround is to right click and pick "Edit IL Instructions". Right click on the exact number so that when you go into the code the portion of the code that you are looking for will be highlighted. All of the numbers are in hex. To continue with the mana pool, you will find "ldc.i4.s" on the left and "0x32" on the right. That is the hexadecimal for 50. Simply change it to anything below 128 and press OK (or if you want a higher number then change ldc.i4.s to ldc.i4 as ldc.i4.s has an upper limit of 128). After that, save the changes that you made to .dll and it's done, your new limit is in the game.

P.S. Keep in mind that if you have an existing save with mages already present then this change will not take effect on them (as the game already used the old values to construct their classes and store them in a save file), but will take effect on any new mages. You can remove the class from your existing mages through dev mode and give them the gem of magic insight and a magic book to effectively reset their class so that they too get the new limit.