IMHO the solution comes out of the Dale Carnegie approach. You need to get the inspector on your side with this.
So you tell the inspector that they are correct! You researched this further and you now understand that in general you cannot run conductors stripped out of cable assemblies in conduit. Additionally (don't say 'but', say 'and', because the 'but' is negating the first sentence; you want to show hot the next thing _adds_ to the first sentence) it turns out that some MC cable is manufactured using inner conductors which are suitably rated and marked so that they can be run in conduit. Because transitioning from cable to conduit (avoiding a splice and junction box) is so desirable, manufacturers have provided a product which permits this while addressing the legitimate concern of having the wrong conductors in the conduit.
Then show the inspector links to MC cable with the appropriate markings, links to the appropriate transition fittings, etc. If possibly also show links to the 'wrong' way of doing it (MC cable without appropriate markings), transitions done by assembling fittings in unlisted fashion, etc.
The point is that you don't want to call the inspector wrong, instead you want to build on their innate desire to be correct in their concerns but you have a solution which does exactly what you wanted to do in the first place while at the same time agreeing with their concerns.
(We can have a deeper debate here as to weather it really matters about the markings on the wire or the use of rigid couplers to combine fittings intended for locknuts.... If the inspector is the sort that actually likes discussion and learning, send them to this forum!)
-Jon