We're not sure regarding why this is happened, as we are using gradient ourselves in our SVG file. If it's not a problem for you, you can send the SVG file that you have created to us (either via email to hello@ar14.works or other method that you are comfortable with) so we can check for the cause.
Viewing post in Custom Clothing Inkscape Gradients
The guide is still incomplete, but you can refer to https://ar14.works/mannequin-docs-customdlc as a start.
Yeah, that is in our sights too, just still thinking about how to make the best user experience for that. Since Mannequin is 2D-based, multiple poses require multiple images so the UI has to be able to explain & accommodate that. Adding logo might be the easiest, but other than that we're still weighing our options for best results. Thank you for your feedback!