how to combine wordpress htaccess on my root domain + php on subfolder

You shouldn’t have to do anything particularly special to get this to work. The mod_rewrite directives in the /subfolder/.htaccess file will naturally override the directives in the parent .htaccess file (in the root).

However, the “problem” would seem to be the following line (in both files):

RewriteRule . /index.php [L]

You are rewriting to /index.php (that’s index.php in the document root) in both files. You need to remove the slash prefix on the substition:

RewriteRule . index.php [L]

You can do this in both files.

You already appear to set the RewriteBase correctly. By specifying a non-relative path in the substitution, you are overriding the value set in the RewriteBase directive.