No automatic way currently, yes. But not "no way" at all. There are plenty of ways to do this: the GM can toggle the Inspire Courage effect off for the alchemist PC in question if they are using splash damage. The PC could put an offsetting modifier in the modifier stack before applying fixed damage, the PC could apply an offsetting one-action effect before applying fixed damage, etc., etc..
I'll look into a way to differentiate damage rolls from fixed damage in the DMG effect when I work on updates to the damage subsystem, probably in a couple of months. In the meantime, like with the many things that aren't covered by automation, or are outside of the current scope of the ruleset, use manual ways to work around it.