In Apache you can put configuration files in each directory: .htaccess files. Every time someone requests a page, however, Apache needs to check for a .htaccess file in that directory, reading and parsing it if it exists. Switching to <Directory> blocks in your main config is much faster, but many places like shared hosting environments can't do that. A solution here might be to add an option to relax Apache's promise of rereading .htaccess files on every request. Instead it could search for them and parse them on startup, and you could either send it a signal to tell it to reload them or it could watch them with inotify.

As a workaround for now, you could use a converter like this one that reads all your .htaccess files and collects them into a htaccess.conf. (You'd run with AllowOverride off.) If you wanted to use this in a shared environment, though, you'd need to parse the config and check that it's safe, not containing an "</Directory>...<Directory ...>" or other injection.