I suppose that if there were some particles or something  that sort of created a "check valve" type of  operation, in which fluid pumped down toward the piston didn't fully return, that could result in a soft, squishy brake lever, with no outward sign of fluid leaking but I'd also expect to feel dragging brakes along the way.
Does the lever come back fully to the front position after you've let loose of it? Â I've had levers that stayed "floppy" and didn't come back forward due to blockage/restriction of the TINY return fluid hole in the m/c - it doesn't take much for this to get blocked up enough to cause problems - it must be cleared out carefully with a tiny strand of copper wire so as not to gouge or enlarge the hole in the soft alloy.
Yes, there is air at the top of the reservoir in the master cylinder, but it isn't supposed to be fully open to the atmosphere to let in more air when the fluid level in the m/c drop from when you are applying the brakes. Â It isn't a very likely scenario to occur, but I think it could happen that under heavy braking it might be possible for it to suck in air this way. Â Â It isn't easy bleeding the air out of the brakes with the rubber bellows and top cap firmly secured in place, correct ? Â At least I can't. Â this is probably a really long shot on the list of possibilities.
Maybe you might be getting leakage back 'round the seal on the piston but not past the , but anytime I've observed leaking piston seals, there was also fluid coming out the end where the lever pushes in on it. MAybe your new bleed screws are letting air in if they aren't fully seated ? Again, I'd expect to at least see/hear some little spit of fluid round them if this were the case, but a gas (Air) can get through places that are still rather water/liquid tight.