Hello,
I noticed the same thing with my own POD Go. If you deactivate all blocks from the effects chain in the POD Go, the input signal from your guitar will loose in high frequencies and presence and will seem to be more boxy (more bass). Input impendance is 1MOhms so it must not be of a problem. There are probably some internal fixed EQs in the POD (intentional or not).
Most guitarists will never notice it. I do because I care a lot about tone presence and meant to use the unit for acoustic guitar too.
Has anyone received a reply from Line6 on this matter?