When splitting signals into bands most of the coloring comes from the phase changes that filters induce. If you want to be 100% transparent, you need 0% change in the phase, for starters.
To achieve this you can use linear phase EQs/Filters to split the signal in bands, as they can filter without affecting the phase (and as far as I know, those are the only devices capable of zero phase change). So you want to either use a multiband splitter that uses linear phase filters, or implement your splitter with linear phase filters/EQs.
The issue with linear phase filters/EQs is that they can potentially induce a lot of latency. From the FabFilter Pro-Q 2 linear phase resolution options, we see that:
Low provides linear-phase processing with a minimal latency. Use only with low Q settings, or when only changing the mid-high part of the spectrum. With a sample rate of 44.1 kHz, it results in a total latency of 3072 samples (about 70 ms).
Medium is a good compromise between low-frequency resolution and latency and we recommend to use this in general for linear-phase processing. The total latency is 5120 samples at a sample rate of 44.1 kHz (about 116 ms).
High gives great low-frequency resolution. If you need to use high Q settings when changing the low end of the spectrum, use this mode. The total latency is 9216 samples at a sample rate of 44.1 kHz (about 209 ms).
Very High gives even better low-frequency resolution. The total latency is 17408 samples at a sample rate of 44.1 kHz (about 395 ms).
Maximum results in very high low-frequency resolution at the expense of a very large latency and possible pre-echo problems. The total latency here is 66560 samples at a sample rate of 44.1 kHz (about 1509 ms).
If the latency becomes so large that your DAW can't compensate for it, you will need to record the filtered bands (bounce, export, freeze track, whatever) and work with the pre-filtered audio (which should be pretty simple to do).
I personally prefer to build my own splitters (a little more complexity for a lot more flexibility) and I use either Logic's linear phase EQ or FabFilter Pro-Q 2.
Another important factor in transparency is how you do the cuts. Make sure you have the same cutoff frequency between adjacent bands, and that they all have the same steepness.
Using linear phase filters/EQs while making accurate and coincident cuts should achieve, in theory, a 100% transparent split.