Nevermind... Turns out you have to drag your alts to base like last season...
meh, I tried that and accepted invite, but I leave base and I cant see it still
And it seems that just setting a char to friend for some reason makes that char marked as invited too (beside the friend status) however the player will not be able to accept invitation. This only shows with the command of ~factioninfo.
If the hideout clearances have been set by the faction leader, they should see it when that character logs on. I've done it this way dozens of times without an issue.