all stations and installations (regardless of them being starports/surfaceports or without a landing pad) influence bgs. they change system attributes (like security or tech level), minor faction property and influence, missions or events available in the system and system economy (via strong/weak links to starports or surfaceports).Never mentioned overwriting Stations, altering Hub's and Padless settlement's, will affect the BGS how? Last time I looked you had to do something tangible, that action would not be one of them.
for example, you removing a military installation (space outpost without pads) will remove a leverage for both bgs and powerplay. refinery hub is the only way you can induce a strong economy link to a starport/surfaceport besides body property. all builds in system introduce and take away some build points (tier 1 build will introduce tier 2 points etc) and if you just remove something, will it destroy all other stations that rely on that point?
those are just some of examples. i believe i could think of more issues if i took some time.