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0) This variant is done on a character by character basis. Some in the party might use this but, not all must. This is why its a 'variant' and is actually useful.
1) If a race has racial spellcasting related to its racial HD, remove that abilities racial power source up to it's RHD. For instance a psychic Illithid would have no psuedo psion levels but a Spellweaver would still have 2 psuedo sorcerer levels. Remember that this variant is done in a character by character basis allowing a psionic illithid to not use this variant while a spellweaver in the party may chose it.
2) BAB may not exceed ECL and RHD's BAB may not be used for prereqs. This makes the RHD's BAB feel like a "practiced BAB" feat since it adds for future, non-BAB-progressing class levels. This obviously stops BAB from exceeding 20 pre-epic. It turns out this doesn't really matter much even if the 21 and 26th BAB gave more iterations. Astute DM's will notice that the ability to hit things a few more times, or even enter non-caster classes early (as casters already do with reckless abandon) is actually a boon to their game's balance. Even if initially counter-intuitive DMs are encouraged to waive this restriction.
3) Skill points from racial HD do not allow a character to exceed the normal 3+ECL max since the HD no longer count towards the ECL. For most cases, this is surprisingly not that needed of a restriction considering the other RAW ways to exceed this cap. Therefore, DMs are encouraged to waive this restriction
4) Skill points for the first level are not added twice. A character with aberration/construct/elemental/giant/humanoid/magic beast/monstrous humanoid/ooze/plant racial HD and one class level may must use the crappy 4x(2+int) for their starting skill point allotment rather than chose their lovely 4x(8+int) rogue class levels as the starting skill points. DMs are encouraged to waive this restriction
5) The racial HD does not get con bonus to HP as class levels do. DMs are encouraged to waive this restriction if they want PCs with above average amounts of HP since HP is way too low compared to the damage both PCs and Monsters can receive anyways.
6) Natural healing rate is based off of ECL and so is not affected by the free racial HD, though this might seem a bit counter intuitive. If you want the RHD to help, it shouldn't make much of a difference, so DMs are encouraged to waive this restriction for any players not abusing natural healing rates. Heck, even if they are they will still be screwed by SoDs.
7) Per level option of LA or RHD counting towards the required level for buyoff. This makes buyoffs happen a bit earlier, which in turn helps the 99% of monsters with over-inflated LAs become playable. It goes without saying that players who use restoration cheese need a single iteration cap on each buyoff tier's level per LA row in the chart.