I haven't tested this yet, but I'd like to post a few of my thoughts anyway. I'll give this a test when I can though.

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I'd like players to be able to move the flags that they own, within a max range of its starting point however. Likely a configuration option set the distance it can be moved. From what I remember a foundation is about 2.5 meters wide, so if you allow a flag to be moved within 15 meters default, players could build under it and move it onto the first or second floor of their base.

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Fortifying a flag now, is a different story, it increases the time it takes to downgrade a flag to neutral before it can be captured as your new flag. Flags should constantly lose capture points, so a level 1 flag would downgrade to neutral on its own after 72 hours. Level 2 would contain many more capture points, letting it last 1 week. Level 3 would require a power generator and lose capture points at half the speed, while having double the capture points lasting 4 weeks. Maybe a bit more to make it 30 days.

Fortifying would require players to visit the flag to raise it to level 2, then feed it spark powder and oil to upgrade it up to level 3, then pearls and metal ingots to max out its capture points. Flags must be neutral to be captured, so enemies standing in range of the flag, would downgrade it faster.

This would stop people from troll claiming things or troll unclaiming so easily. A level 3 flag would take 3+ days for a single player to downgrade requiring an active tribe. Dinos can help the claim timers as well.

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--Flag Points
Neutral Flag: 25920 Points.
Level 1 Flag: 25920 Points.
Level 2 Flag: 60480 Points.
Level 3 Flag: 259200 Points.

--Flag Point Loss
Flag Decay: 0.1 p/s
Player: .5 point per second per crafting skill level. (max at 2.5 p/s)
Large Herbivore: 0.05 p/s
Small Carnivore: 0.05 p/s
Large Carnivore: 0.15 p/s

--Flag Point Gain
Player: .5 point per second per crafting skill level. (max at 2.5 p/s)
Small Carnivore: 0.001 p/s (max at 0.02 p/s)
Large Carnivore: 0.01 p/s (max at 0.05 p/s)
Large Herbivore: 0.001 p/s (max at 0.01 p/s)

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What this says is that if you have 5 large carnivores, 20 small carnivores, 10 large herbivores, your flag will decrease only at 0.2 points per second lasting far far longer, so long as your dinos stay alive within the capture radius.

What this also says is that if you put level up points into your crafting skill, you can capture or fortify flags faster. 5 points in your skill will capture a flag or fortify it as fast as 5 players.

1 player with 5 points in crafting skill and 1 large 2 small carnivores could downgrade a level 3 flag in 26.2 hours, Level 2 in 6.1 hours, Level 1 in 2.1 hours and claim it in another 2.8 hours

Thats a SINGLE player and some dinos claiming someone's base in 38 hours. Add a player, thats 19, add another, 13, 9 and a half. A full team of players could downgrade and steal a base location in less than half a day.

Once a location is downgraded to Neutral, any structures in it can be demolished as if a player was logged out for too long, once claimed, all enemy structures in the claimed territory begin losing hitpoints at 1 per second until destroyed.

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Server config options could be added for enemy detection, alerting tribe members when a friend or foe enters the territory.

Flag options could be added to do this same thing so tribe leaders can decide if they want to be notified. These options would be restrictable in he config so that you can't enable an option if its disabled in config.

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I could add more but, I'm a little tired of typing right now. :P I hope the mod creator gets some ideas from my post at least and that it helps in some way. My valus don't need to be used, I was just coming up with some stuff to use as examples and the way I see that'd be good. Config options are great, everything should be configurable via the configs!