@hasstopher_egen
NOTE:
It is important to understand the context of the technique that you are using with Apple Preview; it is known as "flattening" a PDF. And because you were able to flatten a document with Apple's Preview, that doesn't mean anything in regards of PDF software superiority or inferiority.
Flattening has been around since the mid-90's, it basically is a process that merges many PDF layers into a single layer, and it was released by Adobe Systems on or around 1993.
Nowadays, flattening can also be achieved with any web browser that supports native PDF reading, viewing and printing capabilities, or simply by using any virtual printing device drivers, such as "Microsoft Print to PDF" (if using a Windows box), and also on "CUPS-PDF (Virtual PDF Printer)" if on a Linux box (which can also be used on macOS boxes).
But using the "Export To" method in Adobe Acrobat is slightly more complicated when combined with tools such as Preflight that are mostly intended for analyzing and fixing PDF errors.
While analyzing PDFs with the aid of Acrobat's Preflight tool may fix print production issues, Adobe Acrobat also employs "Distiller", which isn't a virtual printer driver on its own; instead, it's a separate tool that converts PostScript files into PDF files. It operates alongside the "Adobe PDF" virtual printer that is shipped with Adobe Acrobat.
When you "Print To" or "Export To" Adobe PDF virtual printer from any software, the driver initially generates a PostScript file, which is subsequently forwarded to Distiller for conversion to a PDF file.
However, as you've pointed out, flattening with your Apple's Preview software appears to be the most straightforward solution in your situation, as it helps prevent discrepancies or errors that may arise if the PDF document contains corrupt accessible tags that are difficult to fix manually, or even harmful JavaScript code, or any other interactive components like layers. All of these can interfere with various elements and lead to printing issues.
And while flattening is not a breach of HIPAA regulations or within your legal domain, for instance, flattening a PDF into a single image layer can also be viewed as a more secure practice. This ensures that your document retains its intended look and layout when shared or printed, making it more challenging to alter PDF elements.
Nevertheless, in settings where electronic compliance must be adhered to rigorously (such as in the Pharmaceutical industry, FDA, or manufacturing), flattening a PDF is strictly prohibited as it disrupts the structural integrity of a PDF that is necessary for further distribution through electronic invoicing.
Consequently, this is regarded as a violation of specific ISO standards (particularly concerning European electronic invoicing standards), as it undermines electronic signatures or certificate-based digital signatures.
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