There's a lot going on here and I understand your confusion. There are several moving parts. I'll do my best to clarify some things – if anyone sees any errors in what I have written, please chime in.
SSIS package file formats changed significantly between SSDT 2012 and SSDT 2013. Once you have upgraded a package to 2013, you can't go back, unless you have a backup copy.
The upgrade process changes a package's 'PackageFormatVersion' property to 8.
On SQL Server 2012, the PackageFormatVersion needs to be 6 for packages to run.
On SQL Server 2014, the default PackageFormatVersion is 8.
That's all fairly straightforward.
But now add SSMS into the equation. It sometimes tries too hard to be helpful.
If you build an ispac in 2012 and try to deploy it to a 2012 server using SSMS 2014, SSMS helpfully changes the PackageFormatVersion to 8 during deployment. Try to run one of those deployed packages and you'll get the error you got.
I haven't tried all of the possible combinations of SSDT, SSMS and SQL Server to investigate what works, because that would be utterly boring. But if you stick to one of the following combinations, everything should work fine:
1) SSDT-2012 / SSMS 2012 / SQL Server 2012
2) SSDT-2013 / SSMS 2014 / SQL Server 2014
3) VS 2015 / SSMS 2016 / SQL Server 2016