From PF2E Core Rulebook p. 218:
Familiar and Master Abilities
Each day, you channel your magic into two abilities, which can be either familiar or master abilities....
Which is fine and makes sense. On p. 205:
Improved Familiar Attunement
...Your familiar gains an extra ability, and it gains an additional extra ability when you reach 6th, 12th, and 18th levels.
And on p. 210:
You infuse your familiar with additional magical energy. You can select four familiar or master abilities each day, instead of two.
Special If your arcane thesis is improved familiar attunement, your familiar's base number of familiar abilities, before adding any extra abilities from the arcane thesis, is four.
Does having all these features restrict me to picking only familiar abilities, and not master abilities?