Wrong default time zone used

[mauromol]

I'm using Linux Mint 18.3 (based on Ubuntu 16.04).
The default time zone used by the Eclipse flatpak version is GMT, in fact if I look at the "Eclipse IDE Installation Details" | Configuration, I see:
user.timezone=GMT
This is propagated to the applications I run from Eclipse, in fact a println of the default time zone produces:
sun.util.calendar.ZoneInfo[id="GMT",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]

My system time zone, however, is Europe/Rome, as confirmed by /etc/timezone.

Consequences:

• timestamps in Eclipse logs are all off two hours (we're in DST now)
• all the applications I run from Eclipse produce wrong time values, unless of course I change their default time zone or I use explicit time zones

Side question: should I report bugs of the flatpak version here or at https://github.com/mbooth101/eclipse-flatpak/issues?