I think Ubiquitin is absolutely correct here.
There is nothing wrong with asserting yourself, obviously in a proper way, and reclaiming your seat. Of course, the right thing is to try to help find available seats for guests (regardless of whether they took your seat).
In my opinion and [limited] experience, both as a regular and as a guest, this does not embarrass anybody. It is to be expected, and should not even be uncomfortable for the guest.
I do agree that at some point during Davening (in my mind, this point is Borchu), any latecomers relinquish their “rights” in this regard.
As a guest, I never assume a seat is available; I ask someone sitting nearby if the seat I want is open. Being a guest does not exempt you from common decency either. Unless you are completely new to the concept of Shul, you should realize that people have seats.
The place where I usually Daven is very popular, and it is very difficult to get a seat. If I come at a reasonable time to find that a guest has parked himself in my seat, and that I therefore don’t have one (which has happened a number of times), I don’t say anything, but I do think that the guest is wrong.
I once came early to shul, just to find that a guest (whom I knew was a family member of someone who sits near me) had “claimed” my seat with his Tallis bag!
For the record, Rav Shlomo Kluger directly applied the Halacha of Chezkas Karka to seats in Shul. He was asked regarding a Shul that had expanded its building, whether the members’ seats were to be awarded relative to the layout (next to the wall), or if they stayed in the exact location of the previous seat. He ruled that the Makom Kavua was the actual place of the seat because that was the land on which the member had a Chazaka, and not its proximity to the wall.