Often, the ultimate aim is to do more from Perl than just call the main function. Otherwise, your point is valid - and it just boils down to the general C versus Perl consideration.
Personally, I generally don't experience any extra confusion from writing C code in Inline::C. In fact, I mostly find it less confusing to write my C code in Inline, than to write it in C. (Admittedly, I have been using Inline::C on a regular basis for a few years.)