On transforming boltholes into bases:
As has already been noted, boltholes lack a lot of amenities that a permanent base, including sanitary facilities, and are not designed to be particularly defensible. You could certainly build a base around a bolthole, using it as command room, but it would need a lot of supporting structure.
On Recon, MARS, and Science bases:
While all the branches certainly have need of substantial support and command facilities, I don't see that trickling down to the level of most teams. The problem is simply that the field teams are (to my understanding, at least) meant to be mobile. The average team is expected to be travelling over a large area providing services to TMP and the populace as needed. And given the post-war changes it would be extraordinarily hard to predict safe and appropriate places to situate said bases at the team level. Teams may establish bases down the road, but for the first year or two I would expect them to spend almost all their time travelling around their area of responsibility.
On SCIENCE ONE:
In an ideal world, scientific surveys would largely be performed in the field by technicians, not PhD's, and would primarily consist of collecting samples that would then be sent to permanent facilities for any analysis requiring machinery or electronics. TMP is not a perfect world. Transportation is slow and permanent facilities are vulnerable and hard to place. Something like the SCIENCE ONE would be a reasonable (for a game) compromise, shortening the chain between the source and the analysis and allowing strained resources to be repositioned as needed.
On the vehicle itself, I would imagine that the core vehicle would be mostly empty, with electric, plumbing, air, and network connections that would allow it to be configured either as a medical vehicle, biochemical lab, environmental lab, or more esoteric uses. The two halves of the vehicle would share the same propulsion system, none of this halftrack nonsense.
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