Adding a default filezilla.xml should do the trick:
<?xml version="1.0" encoding="UTF-8"?>
<FileZilla3 version="3.15.0.2" platform="windows">
<Settings>
<Setting name="Update Check">0</Setting>
</Settings>
</FileZilla3>
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Rather than doing that, we likely only need to an "XML text" FileWrite to do the same. I haven't tried either way though, so I don't know if it would work.
This was fixed a few releases ago with a default set of settings. We're not forcing it to be set for users as some may want the notification (even though it automatically downloads, which is annoying).
Any users who wish to turn this on or off, it's within Edit - Settings - Update (near the bottom of the list). Set it to Never to never check.
Sometimes, the impossible can become possible, if you're awesome!
Doesn't this force it to be not set check for updates?
[FileWrite8]
Type=Replace
File=%PAL:DataDir%\settings\filezilla.xml
Find='<Setting name="Update Check">1</Setting>'
Replace='<Setting name="Update Check">0</Setting>'