There's no obvious reason to grant the nativeMessaging permission during extension installation for an optional feature, nativeMessaging can be declared as an optional permission since Firefox 87 [1], and Firefox Multi-Account Containers 8.0.2 only supports Firefox 91 or newer.
There could be a bug related to declaring nativeMessaging as an optional permission, though that is not mentioned in the pull request [2], so this was probably an oversight.
EDIT: the minimum supported version was bumped to Firefox 91 in a subsequent PR apparently not for technical reasons, but just to follow guidelines [3], and then they forgot to reevaluate the need for the new default permission before a release.
[1] https://developer.mozilla.org/en-US/docs/Mozilla/Add-ons/Web...
[2] https://github.com/mozilla/multi-account-containers/pull/215...
[3] https://github.com/mozilla/multi-account-containers/pull/218...