Essentially, yeah, we make the base rules solid, so it can withstand a certain degree of tweaking by DMs AND at the same time require minimum tweaks to make it function for a range of settings.
The issue with clerics and deities is a non issue really. Cleric/Paladin power is a construction of their class structure. Mechanically, their deity has no relation to the class except for defining it's theme and fluff aspects, and yes, RAW, your cleric may eventually become more powerful than his patron.
This does not change matters. See for example, the President of the USA. A good number of soldiers could punk him in a straight fight, but they obey anyway. Alternatively, having one of your worshippers hit a level of power equivalent to divinity is empowering for the patron as well, and your former god of shepherds is now the ascendant god of an entire world, with dominion over many things.
Anyway, from a game design and toolkit point of view, we need to allow design room for Small Gods(Shinto kami, Taoist spirits/dragons/demons/deities/immortals, Christian saints, etc), to big time gods(Thor, Amaterasu, Shiva, Pelor, etc). Whether design guidelines for unique outsiders, or a full blown divine rank system, allowance DOES have to be made, or the many DMs and players seeking to include divinities in their game(regardless of which side of the screen) would be forced to either do without, or create extensive houserules, of debatable viability. These don't necessarily need to be combat monsters, nor omnipotent in any sense, most mythological gods(except for monotheistic faiths) are far from omnipotent, though they are still well above most mortals. Yes, even creator gods, being able to use Genesis and Origin of Species doesn't require omnipotence, just a lot of power.
Divinities too broad to be embodied(certain varieties of overgods, the creative principle, etc), don't need to be statted, as they are by definition, untouchable and unknowable(and indeed, a perfectly viable option for DMs who prefer untouchable gods). This section houses the truly omnipotent varieties of deity.