The best-practices section at the very end of the doc says that prefs remain enabled in safe mode: https://searchfox.org/mozilla-central/rev/250f5cc9fb8bdcbb6b23d2a06acfd48addb2f99b/browser/components/urlbar/docs/experiments.rst#624

That's still true for prefs that extensions set on the user branch, but it's not true for prefs on the default branch. This section should be updated in light of the recent discussion around prefs and the top-sites experiment. See e.g. bug 1547670 comment 25 and bug 1578788.

One related question that came up for top sites was whether extensions installed by Normandy are loaded in safe mode. (Extensions you manually install -- like your experiment extension while you're testing it -- aren't loaded in safe mode, of course.) The code for determining that is here: https://searchfox.org/mozilla-central/rev/9bb55ae4d808fc48afcf93f99da6a685265b86c6/toolkit/mozapps/extensions/internal/XPIProvider.jsm#322

Normandy-installed extensions aren't system or built-in extensions, so the answer is no. Might be good to link to that source and mention it.

Apparently add-on experiments are deprecated, so this and some other documentation bugs I've filed are at most very low priority now or just wontfixes. It sounds like they're not outright getting rid of the infrastructure overnight, so I'm hesitant to wontfix them, but that probably makes the most sense. Given the deprecation, I'm no longer planning to work on new experiments docs or changes to existing docs anyway, and we can always reopen them later if things change again.