BeginTable() does insert a \par. I can think of two ways around this (well, three if you count copying unionTables.pl and editing out the \par).
The first would be to capture the output of BeginTable() and substituting out the \par. You could do that in a separate macro, e.g.,
sub myBeginTable {
my $table = BeginTable(@_);
$table = substr($table,4) if $displayMode eq "TeX";
return $table;
}
A second option would be to add some extra TeX to turn the \par into something less troublesome. Something like inserting {\let\par=\relax before the outer table and } afterward to return \par to its usual meaning. I think this is trickier, and probably more fragile.
Hope one of those helps.
Davide