while players on smaller, less populated servers saw an increase in costs.

No, they didn't. At least not in the first wave of adjustments you're referencing.

Patch 2.1 is when they introduced housing and the lowest prices for the smallest servers was 4-5M for a small, 15-18.75M for a medium, and 50-62.5M for a large.

Patch 2.3 is when they added personal housing and adjust prices. If you look at those tables, the large population servers had their prices reduced to the previously low pop prices, and then low pop servers had their prices reduced even lower.

Patch 3.3 is when they added additional wards and normalized the prices across all servers. By this point, gil inflation already had an impact across all worlds, despite smaller servers continuing to have stunted economies.

Now we're in Patch 4.1 and low population servers more or less don't exist in the same form they used to (< 5000 active) because of transfer incentives.