Critterfluffy's answer hits most of the in-universe notes. In S02E12, Shiroe announces to Kinjo & Uru that he's
doing all those things that you mentioned in the title but then spoilered in your question for some reason
- the Round Table doesn't want to keep paying 10,000,000 gold per whatever for its exclusive rights over Akihabara's guild hall, cathedral, and merchant facilities;
- the new arrangement gives them just as much usage rights over what they already have;
- the new arrangement protects them from hostile adventurers taking control of anything in Yamato that they don't currently possess; and
- the new arrangement protects the People of the Land from being exploited by hostile or selfish adventurers down the road, avoiding conflict between them and the good adventurers.
Now, I don't think that Critterfluffy really answered your question because (a) you didn't tick it and (b) CF didn't get far enough outside what Shinroe says in the episode, which you saw and said you couldn't really understand.
It's important to see this development in terms of the shutdown of Akihabara's magical defenses in S02E08. In-universe, it's a nonsensical overreäction given the ease with which Akatsuki's new sword is able to damage Enbart's, which is the only needful thing. At a meta level, however, what's occurring is the partial normalization of the world. Instead of Akihabara being a protected haven where the monsters cannot enter and homicide is near impossible, it's going to be a normal part of a normal world. Monsters won't enter because there will be defenses and patrols; homicide will be avoided (or answered) with policing. This parallels Akatsuki realizing she had to discover her teaching/overskill on her own (same episode) and calls back to S01E05, when they discovered food was only flavorful when you did the work yourself.
Similarly, your problem with Shiroe yielding control is that it's seemingly nonsensical. There's no valid reason for the good guys to not keep the gold cheat on, buy everything, keep it all, use the gold cheat to pay maintenance, and use the leverage of univeral ownership to bring the bad guys and selfish NPCs to heel. In other words, to pull off a still bigger version of Shiroe's trick from S01E09 and be capable of crippling or evading every major baddie. Pace CF, a war with Eastal would be over before it began as the opposing army found it couldn't access its armories, food stores, banks, &c. until it stood down and agreed to some sensible terms. Instead, you have it exactly backwards: S02E12 shows Shiroe 'repay[ing] everyone' by eliminating gamelike powers and destroying every unowned field zone in Yamato. Instead of using the game interface to purchase complete godlike authority over territory, every single piece of land will just be land for the rest of time. It will be open to anyone. It will be used and held according to legal rights established by the adventurers and the People of the Land themselves. It will be protected by their own defensive operations.
This is not at all the munchken or powergaming move here, which shows you that Log Horizon (once again) is advocating real role playing and DIY even when it involves making peace—as Shiroe does in this scene—with being 'weak'.
The move can also be seen as libertarian/democratic and intended to preclude Akiba from eventually degenerating into the inescapable tyranny Nureha established in Minami through her own ownership over the cathedral &c. (S01E25) Whether you buy that depends on how much faith you have in a small town of immortal people being able to work out equitable government amongst themselves. (Fwiw, in the real world with real people, LH's writer skipped out on his societal obligations and was busted for tax evasion.) Of course, in-universe, it doesn't hurt that Shiroe is basically trying to eliminate the game's mechanisms of control and replace them with a society built on mutual agreements and contracts... and he happens to be the only known mage to have developed world-alteringly-powerful contract magic.