You can indeed call Inkscape from PHP - I've done it, see here. Using that approach you can render SVG to all of the formats you require: PDF, PNG and JPG.
If you have the custom fonts installed on your server, then you can render using these fonts - just be aware that this may make you a publisher, and so you will need to ensure you have the license to render using these fonts (or your users do, depending on whose content it is).
Inkscape is rarely installed on web servers by default, so you'll have to use a server on which you have root access, such as a VPS, and install it yourself.
You should bear in mind that there is a security vulnerability in Inkscape that permits user-originated files to steal server files and cause the server to run out of memory (i.e. crash). That fix is now public but I am not sure if it has been released. So, if you are rendering SVG files that have been uploaded by users, untaint carefully.