How do I set default artboard spacing?

In the Rearrange All Artboards dialog there is an option called "Move Artwork with Artboard".  If you turn that option on, there shouldn't be misalignments.

If you want to persistently change the default artboard spacing, you may quit Illustrator, open the Adobe Illustrator Prefs file (locations see below) and change some parameters.

In the Prefs file there is a section called /artnewdialog. In that section you'd have to change the parameter /artboardSpacing 20.0 to something like /artboardSpacing 51.023 (if you want to get 18 mm as the default value for artboard spacing in the New Document dialog). Remember that you have to change the parameter a couple of times in different lines of the /artnewdialog section.

If you then want to change the default artboard spacing that appears in the Rearrange All Artboards dialog, you'd have to search for a section called /ArtboardRearrange. There you can change the parameter /ArtboardSpacing. Save the Prefs file and relaunch Illustrator.

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Adobe Illustrator Prefs - Location:

MacOS: <OSDisk>/Users/<username>/Library/Preferences/Adobe Illustrator <version number> Settings/en_US*/Adobe Illustrator Prefs

Windows: <OSDisk>\Users\<username>\AppData\Roaming\Adobe\Adobe Illustrator <version number> Settings\en_US*\x64\Adobe Illustrator Prefs