you said--"...needs to preflight directly in the Illustrator program. I've done a ton of research and have been racking my brain for the last 2 years and have finally found sufficient workarounds for this issue"
Your workarounds seem time consuming and (possibly) unnecessary for the following reasons:
1. large format printers use 4-8 colors to achieve color (so spot colors shouldn't be an issue)
2. Acrobat Pro has it's own 'preflight' function that works fairly well
additionally (don't know if you know this) there is an add-on to acrobat called 'Pitstop' (google it) that allows just about any change/correction/alteration to be made to a PDF
...and...opening a PDF in illustrator (that wasn't created in illustrator--do you know how to determine this?) can lead to many problems i.e. gradients dropping out, text reflow, etc.
as far as testing your workarounds, seriously, who has the time when there are tools available that make using them unnecessary (this assumes that you have created these 'workarounds' to match your worflow--but a nearly pure PDF workflow should work in this day and age, depending on your RIP and software).
I found another way. I know its dirty but it works 99 on 100.
Import the PDF in InDesign and export it as PDF/X-1a:2001.
If you want to save transparencies, just change PDF compatibility to ACROBAT 5.
Dirty way, but good way.
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