Hi Dane
I suspect that the warning that you are getting can be ignored since, as you know, BLPI is the same as FBI as far as the processor core is concerned.
However beware that it may be possible for perpherals to (optionally) use the FLL or PLL outputs (MCGPPLCLK/MCGFLLCLK) in FBI and maybe the warning is due to that (?).
There are some practical details at http://www.utasker.com/kinetis/MCG.html
In the case of VLPS mode I don't think that you need to worry about whether you are in BLPI or FBI since the PLL and FLL will automatically be stopped anyway.
Regards
Mark