There is no way you can access server files now. You have to create a .php file on external server and link it to your webflow code using jQuery somehow.
Once you create a design in Webflow you can use Export Code feature that will make a .zip file containing your website. You can then upload it to your own server and set it up for your needs. If you build your additional/custom code properly you will be able to use it without a single line change in Webflow. That would allow you to simply make changes on Webflow and export website to your own server. This should also work if you have an external server with your Custom .php files that are linked to your webflow website.