Can I use Enable Media Replace with non-standard file extensions?
WordPress supports uploading the following file types: Uploading Files « WordPress Codex
As long as the file type is supported by WordPress, Enable Media Replace will be able to work as usual. That means that accepting or not accepting non-standard file extensions (for example, a SVG) does not depend on Enable Media Replace, but on WordPress.
Having said that, you can always install a plugin like WP Extra File Types: configure it on your website so you can upload the non-standard extensions you want, and then Enable Media Replace will also be able to replace them.