I basically hacked fileffmpeg.C so it will allow me to choose mov flags for 
(cin-specific) qt 'format'. Of course one can rename all those qt profiles 
too...

int FFOptionsFormatView::handle_event()
{
        Asset *asset = fmt_config->asset;
        char *format_name = asset->fformat;
        char *replace_name = "mov";
        if (!strcmp(format_name, "qt"))
                format_name = replace_name; // fixup
        avformat_free_context(fmt_ctx);  fmt_ctx = 0;
        int ret = avformat_alloc_output_context2(&fmt_ctx, 0, format_name, 0);
        if( ret || !fmt_ctx ) {
                eprintf(_("no format named: %s"), format_name);
                ret = 1;
        }
        if( !ret )
                fmt_config->start(fmt_ctx);
        return 1;
}

basically just three lines. But I have other changes  for this file so diff 
will be not clean.

===
iff --git a/cinelerra-5.1/cinelerra/fileffmpeg.C 
b/cinelerra-5.1/cinelerra/fileffmpeg.C
index ff206b10..d0d58290 100644
--- a/cinelerra-5.1/cinelerra/fileffmpeg.C
+++ b/cinelerra-5.1/cinelerra/fileffmpeg.C
@@ -1938,6 +1943,9 @@ int FFOptionsFormatView::handle_event()
 {
        Asset *asset = fmt_config->asset;
        char *format_name = asset->fformat;
+       char *replace_name = "mov";
+       if (!strcmp(format_name, "qt"))
+               format_name = replace_name; // fixup
        avformat_free_context(fmt_ctx);  fmt_ctx = 0;
        int ret = avformat_alloc_output_context2(&fmt_ctx, 0, format_name, 0);
        if( ret || !fmt_ctx ) {

===

I killed additional lines, but then linecount can be wrong ...
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