Instead of setting Kodi to 5.1 channels try setting it to 2 and enabling the AC3 transcode option in the passthrough section. This may get you to where you want to be without the rest of the mucking about.
Alternatively you might check your AVR settings when playing LPCM audio. It may be that your AVR maintains separate audio settings for that Kind of input and you just need to adjust it to make it the same as your passthrough formats are setup.