That is indeed odd. That's why you just use typed bonuses.
Agreed. The designers are so far going out their way to provide "plain English" descriptions,
and trying to solve usual RPG system problems such as stacking without providing generic rules for them.
Even a moderate amount of bonus stacking is going to be a problem in the bounded accuracy model. Especially with AC boosts or attack penalties to monsters, which are on the edge of being "locked out" on their attacks already (I think they'll fix this).
Could be easily fixed by having general rule of high-level spells over-rule the low level ones, rather than the other way around, and/or using some kind of typing system.
Maybe though this is some clever design testing. Behind each set of spells or monsters, there
might be a more generic rule that they are not showing us, because in actual fact they are running two or three variants of the rule at the same time, writing the results direct into the spell descriptions. And seeing which leads to more satisfying play is probably getting better feedback than playtesters arguing about which kinds of generic stacking rules are "best".
Edit:In the specific case of Prayer versus Bless though, it's not a rule versus direct stacking, because they affect different abilities. It's a rule, as far as I can see, to reduce over-spending of spell slots and decrease likelihood of 5-minute-workdays. In a very minor way, as it only addresses one specific "buff nova" combination (not really a nova, the effects are too minor, it's just removing the temptation to use 2 prepared spell slots when one would do).