Sovereign's Call isn't going to be any more of an advantage than Enchanted Hammers or Propaganda. Unfortunately this change wont have much an impact, since at only 30 population cost an early city is likely the regain that population by the time it finishes building a Pioneer. Pretty easy to get 5-6 growth early on (first ~30 turns)....
The population cost is most significant with new settlements. It basically equates to:
"New settlements cannot build a Pioneer until they reach 30 population, and once they do there is a 30 population growth downtime."
Note1: Faction Prestige growth is distributed evenly amongst all settlements. A Faction Prestige of 6 with 6 settlements == A growth of 1 per city barring things that offer absolute benefits such as Sovereign's Call. Unless a player is not expanding it is pretty difficult to achieve a growth of 5-6 in an individual settlement by season 30.
Note2: While the Capital starts with 30 population, new settlements start with 3. That's extremely significant to Pioneer production. Although losing a net 27 population on Pioneer Production --> Settlement is a little absurd in reflection...
This means most immediately that a player can only really produce pioneers from their capital. It also stacks with Faction Prestige distributing growth evenly amongst all of the settlements. It's basically two birds with one stone, as a player that insists on using newly founded settlements to construct pioneers (likely only feasible with Sovereign's Call) will also be putting off the level 2 city upgrade (the most significant one) for quite some time.
If a player is not expanding so rapidly that individual settlements don't have around ~.5 prestige growth by around season 30 then they aren't really settlement spamming in my eyes. A 30-60 season downtime for Pioneer production and 30-60 season delay for the level 2 upgrade is extremely significant, especially as only the Tower of Dominion offers a natural city growth upgrade for lv 1 settlements.
With this in mind, I'm actually liking the population cost more and more. Gildar is more precious overall yes, but it doesn't deny new settlements from immediately producing Pioneers as a population cost would. Gildar can also be way too easily compensated with wind magic + champions with the merchant skills.
I'm imagining a population cost will give player's strong incentive to wait for their capital to upgrade to a town, then they produce Pioneers from their Capital exclusively after having researched as many growth upgrades as possible. I'm hoping the AI has some way to compensate as it can very easily cripple itself without some forethought... Especially if the population cost is on production and NOT on settlement.
Suggestion: If the primary developer goal was to create a Pioneer production downtime on new settlements, creating a population prerequisite rather than a cost might make a lot more sense. Although in that case, you may as well make Pioneers a level 2 settlement exclusive trained unit. It essentially achieves the same thing and is much more easily communicated. It also completely bypasses all of the odd implications of population cost. This still however favors Life Magic users, although at least Empire won't have production constraints on settlements that are already level 2 (primarily their capital).
This creates another problem however: Any player that creates their capital on a tile with 2 grain has already lost the game.
Addendum: And on reflection, Altar can just use the henchman system to spam "Way of Governer" henchmen. So while Relias seems to gimp them initially, mid-game they have it best of all the factions. If the suggestion is implemented however, this is more or less insignificant though.