Why does my brake pedal go soft after the car sits for a few days?

Pumping it up and having it hold means the hydraulics are basically sound. The soft first pedal after sitting points right at the cups in the master cylinder. When fluid sits under the cups for weeks, they dry out and shrink just enough to let fluid creep back past them. Pump the pedal a few times, they swell back up and seal, everything feels fine. It's a super common thing on cars that sit, and honestly a two year old master that's done this is not unusual, expecially with the modern aftermarket ones. Some of those cups don't love sitting in fluid long term.

Had the exact same thing on my 65 F100 a couple summers back, pedal went mushy after it sat for a month. Bled the whole system twice and it came right back the next time it sat. Ended up pulling the master and honing the bore, there was light pitting right where the cups rest. New cups in that same casting and it's held firm through two winters of sitting since. Worth pulling yours apart before you buy a whole new unit, takes an hour and the kits are cheap.

I suspect you should also inspect the seals within the wheel cylinders, even though you believe they are sound, because minute failures there can allow pockets of air to enter the lines under pressure when the system is cycled repeatedly after extended inactivity. This introduces air that doesn't necessarily come from the reservoir itself, creating that soft initial resistance you describe before the air bubbles dissipate. While the master cylinder is a common failure point for these types of sitting issues, ruling out a slow bleed at the wheel cylinder level is a more economical diagnostic step before committing to pulling the main unit apart. If the reservoir has adequate headspace and the cap seals are intact, the primary ingress of air would typically occur at the cylinder connections, or as previously mentioned, within the master cup mechanism.