Pretty much.
THe way x-wing's rules work is exception-based. I.e. the core rules set up what you CAN do, and specific individual elements provide exceptions to those rules. Unless there's a specific exception on a game element then, the general rule applies.
The general rule is 'when you perform a boost or barrel roll, neither the template nor the ship base can overlap an obstacle. If either would, the boost or barrel roll doesn't happen and you reset back to wherever you were before you tried.'
The specific exception on the Tractor Beam Token reference card is 'the ship base can overlap obstacles'. It says nothing about the template, so the template is not excepted from the general rule.
I'd share the suspicion that it was INTENDED to be excepted from the general rule, but that's not what's actually *written*.