Probably best to go back and read any discussions we've already had, but it will "work" in the sense that you can make recordings and not damage equipment. And yes, since both preamps will already have blocking capacitors (or transformers), it'd work/be safe to use phantom on either or both of the preamps.
The quality of the phantom supply might effect the recording, so using for instance R44 phantom might make the V2 sound "worse" than it would be on its own, or using the V2 phantom might make the R44 sound better than it would on its own (or vice versa). So the comp may not be perfect and might mask some of the differences.
I'm guessing that there also might be a problem with changing gain on one of the preamps, since that might change the impedance at the input, which could affect the sound at the other preamp.
These types of issues will make it difficult to do a pure, unadulterated comparison. But you could run the comp to get some data to use as part of the comparison. Then maybe do a field recording comparison using two sets of the same brand/model of mics, each pair going separately into the two preamps/recording rigs, then do a comparison of the same set of mics going only into one recording chain at a time recording the same material (off say the same CD played back on your home stereo), running each rig separately in time.
Do enough types of comps and instances of comps and you should start getting a sense of the differences between the two devices, but probably no single type of comparison will satisfy everyone that it is fair and valid.