I totally get it. Well... the thing is it works correctly.
We all should not confuse Save and Export, Load and Import. Ai once made it confusing with 'Save a PDF' concept, blurring the line, and making it hard for users to get WHY it works this way. But there are reasons.

PDFs aren’t meant for editing.
PDFs are designed to be viewed and printed.
Illustrator is not a native PDF editor: PDFs can have a bunch of things Ai knows nothing about (videos, forms, interactive buttons, triangular meshes, etc), Ai can creates structures that won’t survive in PDFs (repeat objects, area type texts, dimensions, bleeds — as you said).
PDF is not Ai’s native format. PGF is (that is .ai).
Importing PDFs is IMPORTING.
The magical option just forces Ai to store both native PGF and exported PDF written in one file.
'Opening' a PDF is a lie, Ai either imports one or reads back the compatibility content.
Yeah, I know, we all have to edit PDFs in Ai, because Ai seems the best tool available... I do it myself.

Artboards aren’t pages — in Illustrator. They can overlap, nest... many design tasks relate on it heavily (maps specifically).
There’s also the 'pasteboard' where people can have a bunch of WIP stuff they expect to load fully when a file is read back in — FULL compatibility, right? But PDFs can’t have the pasteboard. It’s either touches and artboard and stays in pages generated, or gets deleted... but only when a PDF gets assembled and exported.

So, again, if you need to have the 'Preserve Illustrator Editing Capabilities' enabled BUT for Ai to clean up stuff that doesn’t touch the exported artboard/page (and thus breaking the 'original Ai/PGF document stays untouched approach') — please upvote the request I shared, https://illustrator.uservoice.com/forums/333657/suggestions/32252662
It would mean people loose pasteboard content, so it is not 'how it should work', but 'how it could work' — thus an option, a feature request, rather than a bug or 'it works wrong'. Remember, user data is sacred. Ai does its best to honor it.

Please raise the awareness, share with colleagues and friends.

Thank you Egor, I’m very familiar with that checkbox.

When you uncheck “Preserve Illustrator Editing Capabilities,” it does indeed remove the other artboards, but it also drastically alters the file’s structure. The bleed is incorporated into the artboard dimensions, and several elements end up hidden or grouped in unusual ways, which makes the file much harder to edit later on.

In production, it’s not uncommon for a printer to ask us for adjustments after the file has been sent (color, font, dimensions, etc.). With a file saved this way, these corrections often become tedious and may even require redoing part of the layout rather than simply correcting the affected element.

My goal isn’t for the AI to clean up the files, but rather for this option to work correctly from the start. I find it surprising that Illustrator doesn’t simply allow you to export a single artboard cleanly, without altering the rest of the document, especially since it’s a widely used software for print production.

For this reason, we still prefer to save each artboard separately and manually rather than use this option, which often complicates print files.

@M-L, when you read the produced PDFs back, Ai reads the original .ai (PGF) data within, and not imports the PDF data.
This is what 'Preserve Illustrator Editing Capabilities' option does — and this one gets enabled based on the PDF preset chosen in the Format Settings dialog within the Export for Screens dialog. If you choose one that does not have this option included (the dialog does a bad job with informing about that, but these are ALL but Illustrator Default, High Quality Print, Press Quality.
And if you want Ai to do a better job with deleting all the artwork that doesn’t belong to a particular artboard when exporting as separate artboards WITH the Editing option enabled, there’s a dedicated request about this: https://illustrator.uservoice.com/forums/333657/suggestions/32252662 — please upvote.

“Export for Screens” doesn't work as intended. Even if you select the PDFs individually, they may appear to be separate when exported, but if you open them in Illustrator, all the other artboards are there.

It’s really important that exporting to individual PDFs works properly, just as the new feature for exporting to individual .ai artboards does. This is crucial when creating multiple print files at once.

This wastes so much of my time! I almost always have multiple pages that need to be exported as single PDF's. Illustrator can save each page as individual .ai files, but cannot save/export individual PDF's with the same settings. And yes, please use the artboard name for each PDF, PLEASE!

Indesign has the option of creating seperate pdf files foe each page, this would be extremely helpful if each artboard could be saved as a seperate pdf in one action

You might want to take a look at File > Export > Export for screens

It does what you're asking for here.
Beware though, it will always use the most recently used PDF save/export settings, regardless what you set it to in Export for screens. So, if you need a particular set of PDF options, make sure to save a single test-document with those before using Export for screens.