Maybe the 1.3 includes don't like the proto/intuition.h that came with DICE
Yes, you have to use a consistent set of include files. Have a look at
https://eab.abime.net/showthread.php?t=68332, it instructs how to install Dice C correctly with the OS 3.9 NDK.
You can use the 3.9 NDK to write programs for 1.3 without issues. Just don't use functions which don't exist in OS 1.3.
(I looked at that .h file and it was pretty empty mostly pointing to other files, and as I don't fully understand prototyping and pragmas... ;-) (obviously)
The proto/*.h files don't contain prototypes. They are (more or less) compiler-independent covers which include the necessary files to tell the compiler how to call OS functions in an efficient way.
The actual prototypes are in clib/*_protos.h
Pragmas tell the compiler how to populate registers with arguments. You might have heard that the OS expects arguments in registers while the C compiler usually puts them on the stack. The pragma instructions tell the compiler to use registers instead. But the #pragma syntax is compiler-specific, so it is not a good idea to include pragma/*.h files in your code. Rather use the proto/*.h file which should know which pragma files to use for each compiler.
It is rather safe to include clib/*.h instead of proto/*.h. It just creates a little overhead in each function call, because it first calls a C stub function which takes arguments from the stack and puts them in registers before it calls the actual OS function.
With the Dice C compiler you might run into situaitions when it tells you "subroutine is too complex to generate code for". In this case the simple solution is to use clib/ include instead of proto/.