The big problem with alchemist's bombs (and splash weapon in general) is how they are written.
Taking alchemist case, for example, the entry related to bombs damage is this:
[...] On a direct hit, an alchemist’s bomb inflicts 1d6 points of fire damage + additional damage equal to the alchemist’s Intelligence modifier. [...] Splash damage from an alchemist bomb is always equal to the bomb’s minimum damage (so if the bomb would deal 2d6+4 points of fire damage on a direct hit, its splash damage would be 6 points of fire damage).
So, with "fewer" words, we can say that a bomb at first level deal only 1d6 + INT damage and the bomb's splash deal 1 + INT damage since the splash damage is always the bomb's minimum damage.
The problems starts here.
We don't know what they mean with "minimum" damage. Minimum of what? Of the bomb's original damage? If this is the case, well, the bomb's splash will always do X damage, where x is the number of dice rolled, plus the alchemist's INT modifier.
And now...what do we do with the static bonuses we can apply to a weapon damage? This is the core of the problem. The splash ignore all the static damage we can apply to a bomb? (smite evil, inspire courage, point blank shot etc etc etc)
In my opinion, rules as written, this point is not clear and since the only "help" Paizo gave us is that Point blank shot faq where we can see that the static damage only apply to bomb damage on a direct hit, not on a bomb splash damage.
What can we do?
Pathfinder, like modern D&D in general, always go for this mantra: specific always overwrite general ruling.
To make it simple; if we have a rule that state "players characters can't run" but you take a feat that say "if you have this feat you can run"...now your character can run.
We can apply this to alchemist's bombs: since a FAQ clearly states that point blank shot does not apply to bombs splash damage...this means everything else similar to point blank shot can apply to bombs splash damage.
The exact opposite. You can take the FAQ as a guideline to choose what can and what can not apply to bombs splash damage.
In reality, Paizo, will never add clarity on this since Pathfinder first edition is ending and Pathfinder second edition will be out in less than an year so, my advice, is to try both. Let the players apply all the static damage they have to bombs splash damage (except for point blank shot xD)...and if you as a group think that's too much do the opposite and let the players apply the static damage only on a direct hit and not on the splash damage of the bombs.