[democrite]

I thought I had it set correctly. I was using a .plist:

Spoiler:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>Label</key>
    <string>com.user.environment</string>
    <key>ProgramArguments</key>
    <array>
				<string>/bin/sh</string>
				<string>-c</string>
			  <string>
				launchctl setenv QT_LOGGING_RULES nextcloud.sync.discovery=false;
				launchctl setenv SIGIL_FORCE_NATIVE_FILE_DIALOG 1
				</string>
    </array>
    <key>RunAtLoad</key>
    <true/>
</dict>
</plist>

I don't really use Save or Save As, but merely command-S so never noticed. Anytime I used a plugin, the save prompt appeared native so I thought it was ok. After trying the plugin to set env variables it looked set ok, but seems I just had to disable and renable again and now it's fine.