DT, the neoprene is quite thin... don't quote me but seems closer to 2.5mm than 3.0mm.  However, I could see your concern about depression. While It is somewhat compact, if clamped for long durations.... I probably would toggle pods as micro differences could be a factor with your Shaper.   The neoprenes are replaceable if they get fatigued... only time will tell... for my use, it would not be an issue.
The filter is designed to keep the sawdust out of the pump. I don't see a need before the pods, however, with use I may find that need and with the way I connect the pods (with Nitto couplers between them rather than one tube from one to the other), filters could be inserted... or even just cut a tube and insert a replaceable filter.

Unfortunately the yellow hood is there to intimidate spiders, as it wouldn't prevent sucking up of idle sawdust.  Though good pickup and I did take on board the comment as I neglected the fact that the pedal activation generated a suck rather than a blow, so I put another filter on the end,

2bsure, 2bsure. Not quite enough room to fit the filter inside the sheath.

If your first cut is too short... Take the second cut from the longer end... LBD