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> and it is not reproducible using openssl s_client
I have determined that s_client is buggy. It will always load the system certs *if and only if* you also pass it a valid custom CA cert (which is the reverse of what's expected).
This is where it happens (in apps/s_client.c):
 if ((!SSL_CTX_load_verify_locations(ctx, CAfile, CApath)) ||
 (!SSL_CTX_set_default_verify_paths(ctx))) {
 /*
 * BIO_printf(bio_err,"error setting default verify locations\n");
 */
 ERR_print_errors(bio_err);
 /* goto end; */
 }
This is why I forced SSL_CERT_* to empty locations in the examples above, so that only the custom CA bundle is used.