Update - It turns out the Mesa libGL.so file was overriding the Nvidia one, in order to avoid destabilizing the system I zipped up the mesa files and replaced them with the nvidia one.

As for using Make, i would recommend trying CMake along with it. As you might know already, CMake is neither Make itself or a compiler, but (very) basically a generator/configurer of Makefiles to use with Make.

Cmake also contain a lot of Find* modules specifically for detecting and locating libraries and dependencies. (basically independent of what platform or architecture Cmake tries to generate your project's Makefiles on).

Example is the FindOpenGL and FindSDL module.

It's also entirely possible to use Cmake to configure/write other files than Makefiles. And also to set and put environment vars into the generated Makefiles. Maybe it could be useful for your problem?

I apologize if i misunderstood your post though.