I did a few more tests this morning, making new characters and casting a Conjuration spell as soon as I was able to.
With SA and the tribunal esp, I get 8 "progress points" per cast.
Without the tribunal esp, I get 6.
Without both SA and tribunal it drops to 4.
So apparently, whenever the game finds an edited value in an esp, it adds that value to the original value in morrowind.esm rather than using the last one. I searched the construction set for the values set in different mods, and found this:
-Baldurdash' Text Patch: the value is also 1.0, but it's marked * which means it was changed and later changed back to its original value (also known as a GSMT if I recall correctly). Pretty weird, since I used TESTool to clean all my plugins.
-adventurers_tribunal.esp doesn't change any value, in fact it changes almost nothing. The only things that were marked where the counts of adamantium weapons and armour. The conjuration skill isn't edited, so my "add changed values to the original one" theory fails here.
-SuperAdventurers.esp changes the value to 1.70
1.00 (original) + 1.00 (Baldurdash) + 1.70 (SA) = only 4.70, so I'd need another changed value of 3.30 to get the 8.00 my game gives. Adventurers_tribunal seems to add 2 even though the value is unchanged, so that still leaves a value of ~1.30 that I can't find anywhere.
Edit: I made a new esp that changes the Conj value to 10.00 and used that with all the "problematic" mods. When I cast a Conj spell now, I get +36 to my progress bar. The maths involved seem to be a bit more complicated than I had first thought...
Edit #2: I edited my esp to give Conj a very low value (0.1). Ingame, casting a Conj spell gave me roughly ~1 point in that skill. Quoting Robert Fripp: "Confusion will be my epitaph"

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