How to merge layers on a page in Preview in Sonoma 14.6.1?

Use the Redact tool instead of creating squares & other shapes. (Preview > Tools > Redact). It will permanently remove whatever you mark. (The redaction becomes permanent when you close the document, so you may want to redact a copy of the PDF, not the original PDF.)

See Annotate a PDF in Preview on Mac - Apple Support for more information.

Do not use export, instead use Print and Save as PDF.

Alternatively, especially if this happens to be a one page PDF, you can export to an image format like png. Once you save a png, the markup is "burnt" into the image.

I used the redact tool recently and it looks like it's redacted on Mac, but everything is still visible when opening the PDF on a Windows computer.

I solved the problem by opening the redacted file in Affinity Designer and exporting it directly back as a PDF.

You could also open the original file in Affinity (or similar software) to edit/redact the info and export it as PDF

Update Sonoma to the current version: 14.7.6. You can do this from the System Settings > General > Software Update panel by scrolling down on that panel until you see Another update is available and the More Info… link. Click that and select Sonoma 14.7.6 (and proably Safari 18.5 too.).

When I click Tools > Redact and then select text, I see the redaction take place immediately. Since Preview autosaves, I then quit Preview and place this PDF in a shared folder with Windows 11 Pro 24H2. I also have an existing PDF with several highlight annotations that are shown in Preview's Inspector. I also place this file in the preceding shared folder after selecting File Print… > PDF > Save as PDF. That definitely flattens any annotation layer as reopening it in Preview, the Inspector shows no annotations in the PDF.

On Windows 11 Pro, I open the PDF with the redacted text in it and it remains very definitely redacted. Then I open the flattened PDF with the multiple colored annotations, and the current version of Adobe Acrobat Reader will not allow me to change any flattened annotation color. It will let me select an annotation and will place a different color border around the existing flattened annotation, but no replacement occurs.

I see no issue with Preview that you claim exists.

Tested macOS Sequoia v15.5.