My 2 pence.
The more 'authority' your heir has, the more chance they have of unopposed succession - they are the 'natural choice'. So I could for example designate them over 2 holdings, 20, or all of them, they'd still be the front runner to inherit the rest through the land's choice if nobody else had any designation, but the odds of opposition, or having low initial stability would increase as the amount of RP spent on designation reduced, with only full payment guaranteeing a smooth succession (as much as anything is ever guaranteed).
Alternatively I could designate multiple people with greater or lesser amounts of the domain, to reduce the cost of wastage if any of them die - but at the same time increasing the risk of contested succession or fragmentation.
Those are bog-standard political risks and rewards to be traded off, the cost is harsh but in practice I'd expect that a realm with high stability and a 'clear natural heir' can afford to be less cautious and simply trust to the will of the gods, whereas a realm in turmoil with no clear successor would need to take the time and effort to formally designate, bend arms, etc to have a reasonable chance of an orderly takeover. A lot probably depends on how strongly identified th eleader is with the organisation - if the leader is known to have a council of powerful advisors then they are automatically looked to as heirs, if the leader takes a lawnmower approach to management succession then there will be trouble.
I see no reason for temple's not to have vassalage or sub-domains, I take it as a given that HA includes Monastic orders, faiths dedicated to gods other than Haelyn, etc - HA itself is simply the core organisation and the political will behind the wider organisation - much as a guild is actually a vast network of smaller guilds not just one type of trade.
You do get the risk of split by assigning vassals - the OIT once controlled all the empire and it has since fragmented multiple times until only a core of 'true believers' still clinging to the centre - but equally you get more actions, RP, etc - it is a risk:reward trade off no different to any other holding type.
In thematic terms it makes perfect sense to give different areas of the church operational responsibility, particularly if they are geographically distinct where the leadership is probably fairly theoretical anyway.
In mechanic terms, the real cost to splitting off vassal domains for a temple holding would not so much be GB (many minor holdings are barely more than break even, particularly when you factor in pandering to local ego's) or RP (like most temples I'm way past collection saturation and would be looking to increase RP income through vassalage) but the increased cost of the ubiquitous BTHL where splitting off a L1 holding adds 1 RP to the cost of each province casting.
If I could stack vassal temple levels for BTHL purposes if I carved out sub-holdings then I'd seriously consider doing so, but if I wind up hemorrhaging RP through increased spend for BTHL then the vassalage RP is amortised and the benefit of the split-off becomes fairly minimal while the costs & risk remain significant.