Okay, I think this is probably as clear as it will ever get, unless someone finds something else in the rules. The text of Racial Substitution Levels on page 145 of Races of Stone states the following:
"To qualify for a racial substitution level, you must be of the proper race. For instance, to select a racial substitution level of dwarf fighter, you must be a dwarf (or be considered a dwarf; see the stoneblessed prestige class in Chapter 5 for an example of what this means)."
The text doesn't say it explicitly, but it stongly suggests that a stoneblessed has some ability which allows it to be considered a dwarf. This is probably the Stoneborn ability, which is as follows:
"At 3rd level, a stoneblessed completes the bond with her chosen race.
- The stoneblessed gains a permanent +2 increase to her Constitution score.
- In addition, for all effects related to race, a stoneblessed is considered a member of the race to which she is bonded. For example, dwarf-bonded stoneblessed are just as vulnerable to effects and abilities that affect dwarves as actual dwarves are (such as a ranger's favored enemy ability), and they can use magic items that are usable only by dwarves.
- The stoneblessed meets any racial prerequisites for prestige classes and feats as if she were a member of her bonded race.
- Finally, the stoneblessed gets an ability based on her type of racial bond."
I had argued that points (2) and (3) are actually the same point, and that the stoneblessed's ability to be considered a member of the race to which she is bonded
for all effects related to race includes the ability to meet the racial prerequisites for prestige classes and feats as if she was a member of her bonded race. However, some others have disagreed.
The text now strongly implies that a stoneblessed bonded to the dwarven race qualifies for racial substitution levels as if he was a dwarf. Strictly by the rules, a racial substitution level is neither a feat nor a prestige class (point 3). Neither is it a +2 bonus to Constitution (point 1) nor one of the abilities based on the racial bond (point 4 - effectively, Stonecunning,
speak with animals and Toughness).
Hence, I conclude that the ability that allows a stoneblessed to qualify for racial substitution levels must be point 2, the ability to be considered a member of the race to which she is bonded
for all effects related to race. So, a general interpretation of point 2 is that any ability that allows a character to be considered a member of a race
for all effects related to race, such as elf blood or orc blood, allows that character to take racial substitution levels for that race. As such, a half-elf
can take elf racial substitution levels.
However, separating point 2 and point 3 appears to create a quirk in the rules. A half-elf can qualify for elf racial substitution levels on the strength of his elf blood, but he cannot qualify for elf-only feats and prestige classes unless those feats and prestige classes explicitly allow half-elves to qualify for them (to be fair, most do). This is because qualifying for these feats and prestige classes is not considered an effect related to race, but qualifying for racial substitution levels somehow is.
It's fine to play with that interpretation. However, I choose to adopt a different one. The way I see it, point 2 and point 3 cannot be separated. If you are considered a member of a race
for all effects related to race, you should be able to qualify for feats and prestige classes as if you were a member of that race, instead of just racial substitution levels.
So, relating back to the topic at hand, going by the interpretation I support, if a monk's unarmed strike is treated as a natural weapon "for the purpose of spells and effects that enhance and improve ... natural weapons" it should also count as a natural weapon for the the purpose of qualifying for feats that improve natural weapons. Such as Improved Natural Attack.