Good point about the miss chance, though that only affects the one character. Alchemist is also a pretty good class for this encounter. However, splash damage is area effect and will automatically do only 50% damage (25% on a save), though a direct hit will still do normal damage (assuming the miss chance didn't get you). The normal 1 point of splash damage from a non-alchemist will do nothing to a blinking character.
It also looks like you also have inflated your damage calculations. It looks like the character has an INT of 22, right? This is why you have listed holy water as doing 2d4+6 damage?
If so your regular bombs will do 1d6+7, not 1d6+10. Point Blank shot adds 1 damage and Firebug adds nothing to damage (it only adds +1 to attack rolls). Minimum splash damage will be 8, but this is reduced by 50% by the blink spell.
Likewise, if your holy water does 2d4+6 damage on a hit then the splash damage will be 7. The rule about splash damage equaling the minimum hit damage only applies to alchemist bombs, not other thrown splash weapons. Holy water normally does 1 splash damage but since you are an alchemist it will be 1 + 6, or 7 points. However, blinking reduces this by 50%, to 3, and a successful save reduces it to 1.
Yes, the idea of him preparing a charge in the corner of the room is exactly what I mean. He certainly is not going to stand in a spot where he can be hit but cannot retaliate. Someone who wants to throw a bomb/acid flask etc. Will have to at the very least stand in the squares just outside the room in order to get him (and from there M will have cover against this attack). As long as they are in the squares just outside the doorway M can attack them, and his bite does a lot of damage.
The idea that Malfeshnekor will stand there and do nothing is pretty silly. That basically turns it into a CR0 encounter.