I ran some tests Flags are basically miniature teleporters that you can teleport to, but not from. Using them on the surface or near the surface of a planet allows you to beam back up to your ship if you need a teleporter. So basically regular teleporters are completely obsolete except for deep undergound bases.
Flags worked deep underground for me, the only thing is that (as you mentioned), they can't be teleported from, so you still have to climb back out. I have one near the core of my starter planet, so I could get core fragments really easily if i ever needed more. The best part of flags is that they are cheap to make, and portable (and editable). You can bring a stack of them along, just don't forget to activate them after you place them. Just have to click on it to name it basically. You can pick it back up when you're done, or just leave it there.
I still make ample use of full teleporters so I can travel from one end of my compound to the other very quickly from indoors, underground, etc. Because yeah. A flag is a nice warp-to device, but it is useless as a warp-from. And at my deep storage facility at the planet's core?
Since they are a teleport destination only, they're really useful for stuff that you want to come back to loot but not necessarily build around. And since they are destructible, you can reuse them with abandon. Climbing out is still necessary, but has anyone else come to enjoy the rapid pace of using ropes and grapple devices to ascend? Hellevators can be useful if you've mastered the waterfall-jetpack exploit.
Mioved to general help. Remember if you have any doubts on vanillia features - best place to put it is general help. That way you can mark best answer and it will benefit others who have similar doubts.