This seems to be because Special:ExportTranslations doesn’t allow exporting discouraged message groups (rETRA src/Synchronization/ExportTranslationsSpecialPage.php:135 (at 6fd67a881b9e)), but apparently the JavaScript-based message group selector doesn’t consider this (if you disable JavaScript, you can’t select the group in the first place). So there are two ways to restore consistency:

• Teach the JS solution to ignore these groups. This obviously doesn’t help you achieve what you want, but at least does so consistently. (However, you can work around the limitation by encouraging translation – even right now, without any code changes.)
• Teach the PHP solution not to ignore these groups. I don’t know what problems this would cause, but I suppose this limitation was introduced on purpose. (Maybe just to make the dropdown list more usable? With the JS-based group selector, this is less of a concern.)

Limitation was introduced in rETRA55d9157f81aa6a49ec01eabba16a5f2d6a48e23c without explanation. I don't think it's necessary.

Change #1016338 had a related patch set uploaded (by Abijeet Patro; author: Abijeet Patro):

[mediawiki/extensions/Translate@master] Allow discouraged groups to be exported

https://gerrit.wikimedia.org/r/1016338

Change #1016338 merged by jenkins-bot:

[mediawiki/extensions/Translate@master] Allow discouraged groups to be exported

https://gerrit.wikimedia.org/r/1016338