To use a very basic example, say I have the Chroma with the Doom 2 in as the whole effects chain. Bass > Chroma (Doom 2) > Amp. In this configuration, if I turn on the band pass filter to get a wah sound and then turn the mix down to retain low end, what I get is the fuzzed-out Doom 2 sound with the completely unfiltered, unfuzzed clean bass sound mixed back in. What I would prefer (or would like to have the option for) is to mix the unfiltered return from the Doom 2 back in, so that it sounds more like a complete fuzzed wah sound (with the massive low end that the Doom 2 provides) as opposed to a fuzz wah sound with clean bass mixed in.
This basically only only applies to using the band pass mode, but for me it still impacts the sound enough that my solution was to run my Octabvre before the Chroma for only the purpose of affecting the clean mixed signal.