Indeed, the issue perhps isn't that founding later is a disadvantage, but founding earlier isn't enough of an advantage to make you want to found with debt. I propose instead that this issue would be fixed if the debt timer ticked down slower when debt became smaller and people start placing HQ's. If someone pays 20K debt for a headstart it should be a real headstart rather than about 10 seconds. If this changes to how I suggest then the metagame will naturally evolve and people will have to actually pay for their spots, making them take on debt that ohers founding later do not have to.
It's really map dependent, I think. On a low and sometimes medium resource maps there's usually no more than 1-2 prime spots, the rest is subpar. Thus the headstart is huge as is and is worth 20k (or w/e) debt. Granting even further advantage to the prime spot owner would be a game killer. On the other hand, on high resource or just lucky maps there's multiple good spots and it only makes sense to wait in order to avoid debt and receive the extra claim.
The main reason I do believe the debt timer should be slower by the end, is that players' successful founding is tied to latency and their computer specs. For example, in an 8-man game, if your machine is on the slower side and the connection to host is not the best either, it's extremely difficult to switch from plan A to B to C etc, because it's physically impossible to scroll the huge map fast enough. Add that to the very fast debt countdown in an 8-man and you are pretty much forced to take the debt even when there's no strategic reasoning behind that.
That's why I feel the map generation can use more resource balancing. The founding should not be about fast clicking or higher end rigs, but about decision making. We can all agree on that. In one of the streams Cubit suggested pre-game bidding for founding locations. Perhaps this particular idea is a bit hard to implement, but I like the general concept. It's not fun for anybody when the game is over within 30 seconds and this happens in 10-15% of the games if not more - a bit too often to my liking.
I am not a big fan of mirror maps (imo, they are boring) but they are fair at least. Introducing them as a custom option might be helpful for those who prefer fairness over excitement of rolling the dice.