Web:
1) After 48 hrs w/ 90 deg temps, it should have set enough to walk on. If you could 'dent' it by walking on it, so could the crew that dropped the liner, so I'm thinking it would have been noticed (though it's easier to notice these things when barefoot). The spots should not stay soft, nor resoften in subsequent rains, however if the rain came quikly enough and in sufficient amounts to 'channel' the surface - the bonding cement may have washed out and wet vermiculite (with no cement) is 'mushy'. (I have seen pools where the cement has slowly been washed out over the course of 10+ years of water continually channelling through it, leaving behind 'mush') As a general rule for cement mixes, the material reaches full cure after ~28 days, at this point it is as hard as it will ever get and deteriorates VERRY SSSLLLOOOWWWLLLYYY! , but for practical purposes a day or two allows use (always dependant on the situation/ conditions)
2) An area like that doesn't sound like the mix was improperly trowled, it sounds like someone left a pile of debris from sweeping the pool (however, I wasn't there to see what was done). If it is just some vermiculite peices that didn't get fully removed, you can push them down with your thumb and they'll flatten out - if you feel any sharp edges while pushing or if it's hard and won't push down - STOP and have it addressed by the PB ( they'll have to partially drain the pool and remove/ fix it)
3) That is the extreme case of "no noticeable dips or humps"! As long as it transitions up and down smootly, no problem - other that 'Webfoot's Isle' is taking up 2/3 of the shallow end. If you can live with it and it hasn't caused the liner to wrinkle - I'd say this is the 'bargaining chip' for you when you talk with PB (ie. fix 1 &2 and I'll be cool about 3) - I must point out that it would have been 'glaringly' noticeable if someone had just looked at the shallow end at 'eye-level' from the 'break' (the transition from shallow to deep end).
I, again wish you the best with your new pool! If I've been unclear or haven't fully addressed your concerns, feel free to ask