hi u can configure site to site vpns between 2 peers but with the limitation that the subnets behind the peers will not be encrypted.
in transport only the ike endpoints and the traffic between them can be encrypted.
regarding nat if u are using ah as the protocol for ipsec then no natting can be done anywhere as in ah the entire ip packet is authenticated means hashed so any changes in that will result in dropping of packet by the other peer.
if u are esp in transport then natting should not be a problem cause with esp the transport layer and above is encrypted and layer 3 header is intact.
hope this helps.
regards
sushil