It is OK to modify an E-LSA to your hearts content AFTER it is certificated and the 5 hours are flown off as long as the aircraft still meets the definition of LSA. Modifications do NOT have to meet any ASTM standards or be portable. Your certificated E-LSA is an experimental airplane and can be modified just like an amateur built experimental airplane. Sure, you might have to submit paper work to the FAA for major modifications, but that is a minor issue and will not prevent a person from making changes to their aircraft. See my posting
http://www.vansairforce.com/community/showthread.php?p=306048#post306048
If you want to get the facts directly from EAA headquarters, call Joe Norris at 888.322.4636 Extension 6806
Joe Gores