The problem has been resolved, files came together once I added the CMYK elements in with the Spot White ones, though it took a few tries to get it right.
Saving files out as Tiffs (with spot whites) like Bobby H has noticed, it can be inconsistent which is why I thought reaching out to this community would be a smart idea.
The reason I do not like printing from PDFs is due to the inconsistency I've seen when they are saved out of programs like InDesign. Note that in some of the places I've worked (franchise sign shop), we get tons of walk-in customers that will take a PowerPoint file and save it as a PDF, or take a Publisher file and save it as a PDF. I can't tell you how many times I've seen color shifts, or shadows disappear after opening up the PDF in Illustrator. My current employer is a very custom print house, we are very keen on color and we prefer native files above all else.
We don't print brochures, flyers or catalogs, we have no need for InDesign files. All of the artwork that is submitted to me could easily be produced in other Adobe programs with more success, which means more consistency throughout our internal process. PDF may be the most ubiquitous method of sending files, but it doesn't always lend itself well to editing. At the company I work for, we discourage clients from sending us PDFs simply because we can't guarantee the results. I understand and know that Onyx and myriad other RIPs support PDF; I've printed from them at other shops. However, the company I work for requires native files if at all possible because we do a great deal of color correction and matching (we do a fair amount of fine art reproduction). There is no guarantee that a PDF will work for every pre-press tech, or every application unless you are the one that produces the PDF.
We have to build our files in a certain way to maintain a consistent workflow in order to reproduce orders in the future, we maintain it because if an issue were to arise, knowing exactly how your files are created is paramount to locating and correcting the issue. Yes our RIP reads files a particular way, it's an old machine with an old RIP. I am in no position to purchase a new one, thus I work with what I have. I had minimal training from my predecessor but she left me with a few rules to follow. One of them was only sending Postscript files or TIFFs to the Durst, TIFFs preferably because we skip the step the RIP takes by converting the file to a TIFF.
tl;dr: problem solved