Squawking 7700 summed up the differences between MGIR & FI(SLMG) nicely
here. See also this
BGA web page. People get confused because the BGA run the courses but the rating is issued by the CAA.
Forget about JAR licences, they are no longer issued. You could fly with every instructor known to the CAA & none of those hours would count towards the issue of a JAR licence because no-one is going to issue one. Counting hours towards an EASA licence is also irrelevant, as the CAA are not yet issuing LAPL(A)s for TMGs (
AFAIK.) They are still issuing NPPL SLMGs; the holder of an NPPL SLMG has until April 2015 to convert this into an EASA LAPL(A) for TMGs.
If you want to fly a Cub you will need an NPPL SSEA or EASA PPL or LAPL. The NPPL can be used in France if backed up by an EASA class 2 medical. You can add an SSEA rating to an NPPL SLMG & (eventually) add SEP rights to an LAPL(A) for TMGs. Or you could go for the appropriate licence straight away.
AIUI the requirement for a type certified engine stems from the conditions of an AOC. You don't need to have an AOC to be an ATO.