If all you are using Perl for is to call your main function ....

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.

...write the whole thing in C and avoid the confusion all together

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.)

Cheers,
Rob