After further testing I could find a workaround by modifying the html2mobi script, adding:
$tree->no_space_compacting(1);
just before the "$tree->parse_file" in "sub one_html_file". (A similar addition is needed in mobi2html.) Then I found
this:
Fixed HTML::TreeBuilder to not remove where it shouldn't, using patch supplied in RT 17481.
That's dated in 2006. The only TreeBuilder.pm in my system seems to be from Perl 5.8.2, dated in September 2003, so it is quite possible this "bug" is already corrected in newer systems.
Edit: I found a way to add the </p> as well, using "my $html = $tree->as_HTML(undef,undef,{});" instead of "my $html = $tree->as_HTML;" in mobi2html.