This is how it should be but, unfortunately, it isn’t. I just tested it again with a second player because I thought it might work differently with my own alts…
Char1-Account1 and Char2-Account2 are a member of the same guild. Char1-Account1 walks into the beacon of Char2-Account2 and generates footfall.
Char3-Account1 and Char2-Account2 are a member of the same guild. Char2-Account2 aligns her beacon with the guild (aligned, not guild controlled!). Char3-Account1 walks into the aligned beacon of Char2-Account2 and triggers no footfall.
Char1 and Char3 have zero permission on the beacons of Chat2-Account2 and aligning a beacon to a guild does not give you any permission.
Basically, this problem still exists: