The whole mini-split scene has been a nightmare for many inspectors and electricians.
Many of the systems are foreign and many are covered by various listing agencies. Some come with instructions calling for wiring methods that are not NEC allowed (cord), most ignore the need for a disconnecting means on the interior motor and some of the larger units ignore the fact that the smaller conductors to the interior unit do not, on some units, have overcurrent protection.
Add to that a myriad of "special" instructions added by the manufacturer.
I talked with some UL folks concerning some of the problems where manufacture instructions clashed with NEC and they noted the units were not UL listed but rather ETL. ETL folks said they would "look into it" (twice).
FWIW, I know of several Mitsubishi splits that have had switches added and wires spliced that seem to be operating fine... (not saying your unite would)
I do agree with most of you on the fact that splicing is not likely to be an issue. The use of a three pole disconnect switch for the indoor unit is optional, according to the manufacturer (req'd by the NEC) and I cannot imagine it having much different of an effect than a properly spliced junction. What I do know is that Mitsubishi takes warranty claims VERY seriously and prides themselves on their quality. They say their warranty claim rate is 0.05% of all units and industry standard for spilt systems is 2%. It is my opinion that they do not want splices in their system because too many HVAC guys don't know how to properly install them, as one responder commented. They market heavily to end users and their reputation is on the line when someone does an improper install.
That being said, this is only my second install for these units (the first was a residential application where I used UF to be able to meet both indoor and outdoor NEC code) and I am doing 7 of them. I do not want any issues that a field service rep would deem a problem, as it is 7X the problem for this particular job.
So in light of that, I will be doing a single, unspliced run and am thankful for the feedback given thus far and would appreciate any additional feedback as it relates to the original post.
Oh, and Augie, a quick comment on your post regarding the indoor unit wiring not being protected at an appropriate level if it is smaller than the outdoor unit's power circuit: The circuit boards for the Mitsubishi units contain a couple of 7A fuses to protect the 14 AWG wire powering the indoor units. I had the electrical inspector ask the same question and this is what the manufacturers rep told me and I later confirmed by the line drawings in the product docs.