I would imagine...
Perhaps, from a fanon/canon suspension of disbelief-type perspective, power generators are placed outside because the energies from both the annihilation of hypermatter and the ray/particle shielding would clash and cause problems. Idk, maybe it's inefficient or something.
In terms of balance it makes a degree of sense when the generator is also hidden away in a little corner of the map, certainly makes for fair opportunity. If the shield generator is easy to reach then the whole idea is a waste of time and it might as well be shielded, but if it's well defended and very hard to get to on the other hand then it's a good bit of fun for the methodical commander.