WotC has a history of poorly-worded or otherwise incomplete rules, and Unearthed Arcana is full of them. Sometimes they're meant to be open-ended to allow DMs to fudge things a bit, but given a rule set the size and scope that D&D 3.X turned out to be there are definitely going to be screwups, and the players and DM are expected to have their eye out for those.
One of the biggest offenders right in the PHB is monks don't technically get proficiency with unarmed strikes. No one in their right mind (and I expect many who are in their wrong mind) would play it that strictly though because it's incredibly obvious that it's an oversight given the other class features and the monk's kit in general.
That's the main reason I never play Read As Written. Whether a rule will work and be reasonable is very likely to be up to the players and DM and how they want to play, including repercussions of certain spells.
Minor Creation, for example, can entirely screw with an area's economics by making a sizable amount of whatever vegetable/plant matter the caster wants. Even simple sugar and pepper have quite a high price in D&D compared to what we're used to.
As far as the interpretation of the Unique Spells for those prestige classes go, simply opening up the whole list of the normal class for only taking a single level in the prestige version could cause problems depending on the group. Some of the spells the bard, paladin, and ranger get later on are not "balanced" around the same spell level of wizard or clerics. And that goes both ways into possibly overpowered or definitely underpowered territory. An example of the latter is Cure Light Wounds being a 1st level spell even for paladins (who get it at 4th level, so 3 levels later than most casters) but rangers for some reason have it as a 2nd level spell and is thus only castable at 8th level of all things assuming the ranger has a high enough wisdom to get a bonus spell slot at that level because normally they'd have 0 2nd level spell slots then.
It comes down to taking the rules with a shaker of salt (not just a grain will do) and making sure to come up with reasonable rules interpretations that will work for the way the table is playing the game. Quite often something can be pulled out that can be broadly applied to pretty much all games, but others not so much.
Note that paladins technically have a 3.5 unique spell with
Favor of the Martyr. However, in 3.0 it was printed in Magic of Faerun as
Favor of Ilmater and still retains
that name in the 3.5 transition book Player's Guide to Faerun.