Hi,
Thanks for buying pro. The free trial is always recommended
I think Visual Micro for Atmel is currently at Arduino 1.6.9 which is sometimes important. 1.6.10 and 11 have only recently been released so it always takes a few weeks before we submit a new gallery request with a new release.
Minor note: That said there should be much difference and because you are using the zero the core is a different download so again should be fine.
More importantly Visual Micro is Arduino compatible and works to the Arduino guidelines otherwise can't easily be supported.
The Arduino build rules are as follows:-
1) The Arduino Core is built into an archive files or as stipulated by the platform build definitions. The core build does not have access to library or project code.
2) The Libraries are built. The libraries have access to core include paths and include paths for all other included libraries
3) The project code is build having access to all related include paths.
Unless I have misunderstood, you are going to have difficulties trying to access project code from core, it's the wrong way around.
Because Arduino combines .ino code into a .cpp file prior to compile the compilation happens in a hidden temp folder. This means that the project code has to be copied to the temp folder and then compiled. This changes the include paths so requiring this automation is very difficult for users to have any control or affect over.
Lastly one thing that might help is to use the visual micro project property compiler
extra flags. You can add include paths that will be applied to all build stages using the -I switch. But it doesn't support relative paths, does not affect what code is compiled, is simply a way to include some extra paths during build. Is a bit cumbersome and is for experienced users who can understand what the feature does.