You can force the compiler settings Perl and ExtUtils::MakeMaker use by editing Config.pm. But doing so is quite unwise, especially when trying to mix -MTd and -MD, as the libraries and modes linked by these two are substantially different. You will have to find a way to link all libraries with the same settings, whatever that setting may be that works for all of your libraries. You might find that compiling your own Perl is more convenient to achieve your goal.

All of these flags are compile time settings and change how the Perl executable itself (perl.exe and perl58.dll) is created, so changing any of these is best done when compiling your own Perl.

Can you write a thin wrapper around the static libraries and compile that for dynamic linking?

I've never tried this, this is just a wild idea. You've been warned. ;)

package MY;

sub cflags {
    my $inherited = shift->SUPER::cflags( @_ );
    if( $^O eq 'MSWin32' ) {
        $inherited =~ s/-O1/-O2/sg;
        # set static linking to crt
        $inherited =~ s/-MD/-MT/sg;
    }
    $inherited;
}

sub const_loadlibs {
    my $inherited = shift->SUPER::const_loadlibs( @_ );
    if( $^O eq 'MSWin32' ) {
        # set static linking to crt
        $inherited =~ s/msvcrt\.lib/libcmt\.lib/sgi;
    }
    $inherited;
}
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