I've been wondering about that same question. It seems that, yes, the default magnification option is entirely useless, since the default is set by the document, not by your preferences. I'm puzzled why Acrobat would have an entirely non-functioning, basic, feature, but there you are.
So I think what we need is a macro that would, for every document, do the following:
1. Open up properties.
2. Change the magnification to 100%.
3. Save the changes.
4. Go back to viewing the document.
I don't know if Acrobat has add-ons, or if macros are possible, tho.
There must be literally millions of users who want this feature. My eyes are getting old and I read mathematical documents, so starting at 69% is bad for me. I'm not sure who it's good for, actually.
Here are a few other pages that are relevant but don't solve the problem:
This stackoverflow page has a command-line way to open files at 100% :
AcroRd32 /A "zoom=100=OpenActions" filetobeopened.pdf
Of course, doing that every time instead of just clicking on the filename in Windows would be impractical.
This file has general info on command-line methods.
This thread has the obtuse replies of someone from Adobe to a user who wondered why users aren't allowed to set default zooms. THe Adobe person say that would infringe on the freedom of the document writer to impose a default zoom. As if more than tiny number of writers cared!
Regarding the OP:
"How can I set the default to open all PDF's at 100% zoom magnification?"
With Acrobat Pro, run a Batch Process (Sequence)/Action to run the "Open Options" sequence.
This sequence permits setting the values for all items under the Initial View tab of PDFs' Document Properties.
Regarding a PDF's Document Properties > Initial View:
Visit an open PDF's Document Properties (Ctrl+D, Cmd+D). Go to the Initial View tab. The top pane (Layout and Magnification) permits configuration of:
Navigation tab: Page Only | Bookmarks Panel and Page | Pages Panel and Page | Attachments Panel and Page | Layers Panel and Page
Page Layout: Default | Single Page | Single Page Continuous | Two-Up (Facing) | Two-Up (Cover Page) | Two-Up Continuous (Cover Page)
Magnification: Default | Actual Size | Fit Page | Fit Width | Fit Height | Fit Visible | Magnification percentages (25% to 6400%)
Configuration settings other than "Default" dictate how the PDF is viewed initially.
The settings for all values in all panes in the Initial View may be established for one or many PDFs by use of a Batch Sequence/Action (Acrobat Pro required).
This functionality is utilized in an enterprise environment where large document collections are deployed in a LAN/WAN "eLibrary" to provide a consistent initial view to end-users.
It also provides a content author a mechanism for establishing the initial view for *their* deployed content (such as PDF document collections distributed on optical storage media).
As to the typical default Initial View for a created PDF:
When a PDF is created via Acrobat the PDF document's default Initial View for Layout and Magnification is:
--| Navigation: Page Only
--| Page layout: Default
--| Magnification: Default
--| Open to page: 1
Regarding the Open Parameters document — While this document does provide a few command line options the document's primary focus is the use of a URL to open a URL's targeted PDF's initially opening.
Worth noting is that the document is specific for URLs and not applicable to UNC links (links with a LAN/WAN).