Having two types of uniforms in service at the same time just doesn't seem that crazy to me I guess.
While I agree that it's no big deal, a case could be made based on the definition of 'uniform' as being something that... well, has got uniformity
. There's almost no point in having a uniform if every other guy we see is wearing a different version of it. Really, it ought to have been an all-or-nothing approach. Give everybody the old uniforms, or give everybody the new uniforms. Don't split it down the middle.
I assume the 'real life' explanation is that Rick Berman decided the unused versions seen on the Playmates figures looked bad on screen, and made an eleventh hour decision not to use them... but still wanted to transition to a new look.