Province bonuses for levy sizes are functioning properly. Easy test for this is to play the Christo-Zalmoxian Artorius family in Brythonia. They have an overall +20% to all levy sizes, and an extra +30% to city levies at the province level.
These bonuses are working fine, but on the character sheet there's an extra +25% to city levies, +10% to castle, and +5% to temple levies that doesn't seem to be having any effect at all.
Thanks a lot for reporting!
Every thing is working as intended. But let me use this opportunity to clarify how things work with these various modifiers.
Basically there are two kinds of modifiers, quite different in what they represent and in their effects:
1 - the province modifiers work as you describe, by directly impacting the size of levies of a province's holdings (all of them or specifically some types if specified so). They represent the way religions impact the socio-economic "infrastructure" of military mobilization. So for example, whatever a leader's religion is, Graeco-Roman cities provide more soldiers as there is a tradition of armies based on urban militia.
2 - the character modifiers represent how a religion impacts the political "superstructure" of military mobilization, i.e. how the ruling elite know to mobilize their realm's potential manpower. They impact the % of levies made available by the corresponding vassals. A bonus on city levies in the character sheet means that you have a bonus on the % that cities let you access their militia, exactly like the levy laws. So, for example, whatever the local religion is, Graeco-Roman rulers will rely more on cities to provide them soldiers than rulers of other religions.
(Now, technically, the game shows you two modifiers of the character screen, and makes a poor job at explaining them. One is called "Burgher Vassal Max Levy": this is rather clear. The other one is called "City levy size" and is put much lower. Actually that one should be called "Burgher Vassal Levy". It is the one actually raising the percentage of levies a vassal of a given holding type will let you raise. In general both modifiers for a given holding type are raised in an equal proportion, not only in my module but in almost all mods I saw, as you need both to be sure the increase actually occurs. I think this is where you got confused by the poor interface wording and seemingly redundant modifier.)
In most cases, the 1- local and the 2- character (or "political") modifiers work in the same direction. But this may not be the case in very specific combinations, often syncretic ones with an Ascendant of a different kind than the primary Civilization. One interesting example among coded religions: Tengri-Buddhism:
- local Tengri-Buddhist monasteries train many monks in the martial way (this is a Buddhist characteristic, maybe a bit "Hollywoodian", but quite fun I feel...) and get a +50% in the size of the local levy
- A Tengri-Buddhist Ruler, however, does not really interact much with temples (and cities) as much as he mobilizes manpower from rural areas (i.e. castles). So, he gets a malus in his ability to mobilize the great potential that Buddhist warrior monks represent. A true Buddhist ruler would have be aligned and would have got a bonus.
In conclusion, in your case, the character +25% bonus on cities helps you get more of the extra levies your city vassals get by their local +30% bonus on levy size. Just pay attention to you relationship with burghers not to spoil this potential little extra!