There have been several Le Mans entries that had flags of the auto mfgr. Here are a few that come to mind:
1) 1999--Nissan R391 (#22 and #23) has Japanese flag on entire rear engine cover.
2) 1976--Spirit of LeMans '76 Greenwood Corvette (has the classic Spirit of '76 depiction of two drummers and flutist marching w/ US colonial flag.
3) 2002--Audi R8s #1, 2, & 3 and painted in silver with each car painted with one color of the German flag (black, red, and yellow)
4) 2002--Panoz LMP01 #11 & 12 is painted in red, white and blue livery with stars and stripes (USA).
(cars painted with flags from team location)
1) 2000--Panoz LMP01 #10 Den Bla Avis was painted with a Denmark flag of the sponsor, not the auto mfgr.
2) 1996--Ferrari 333 SP #17 Racing for Belgium was painted with Belgium flag since the team was sponsored by Belgium people, but not auto mfgr.