Hi TheLastCayen, I found the same thing awhile ago. I am struggling to remember now but I think I eventually found that I fpcmake was not really intended to work as we both read the docs.
Have a look at my bash script
https://github.com/tomboy-notes/tomboy-ng/blob/master/package/package.bash its quite busy because it builds Windows, and Linux in several different formats. You are interested in only the first function, BuildIt(), it uses lazbuild and reads the Lazarus project file to build each binary based on the Lazarus Project Modes.
You can go one step further and call fpc directly if you like, In the Project Options there is a button across the bottom of window (called, from memory) "show options", its only there in the compiling config sections of project options. It shows you all the options that will, eventually be passed to fpc.
I have a script that does that in
https://github.com/tomboy-notes/tomboy-ng/blob/master/tomboy-ng/buildit.bash, bit more complicated in that it assumes you don't have a working Lazarus, first it builds lazbuild and then uses that to build KControls (that my project uses) and then builds the main app with fpc. Its has proven to be a bit maintenance heavy ...
Davo