You can simply to get the flattening done, but since there are no color profiles and the fonts are not there (probably), then it won't solve those problems.
Assuming your keeping the color intents the same in Acrobat and Illustrator, there is no reason you would see a difference in output.
Publisher should not be used to print to anything more than a desktop printer. Even their (MS) lead print engineer says to use PDF
If I already have the PDF file could i save it over as that PDF/x?
Caus ei relaise when I print from PDF it is lighter than printing straigth say from AI or Publisher
The answer is always to use PDF/X, it doesn't matter what printer, if it has a PS interpreter, PDF/X is the answer.
From a compatibility standpoint, go with PDF/X3, purely because nearly every printer can interpret it. PDF/X is the solution to incorrect fonts (not being properly embedded) and dark backgrounds (printers don't understand transparency, they attempt to print the nothing, and you get shadow boxes around images)
Is there a PDF preset file that I can have our Creative Suite users use when creating PDF files for printing to a Freflow RIP>ColorPress 1000?