Came here hoping for a fix for this exactly. Don't want to draw weird invisible shapes to use as hotspot links. Hope there's a fix for this soon.

Beautiful site my friend! Quick FYI the text in the opening about section is cutoff on my iPad.

If the benefits of keeping everything together are in any way about presentation you can use zeplin to help. That way you can split up (in the beginning, later, mid way through the project, whatever your heart desires) the Sketch files and just publish everything to the single zeplin project. If it's a really dense app with a lot of flows, using the tags in zeplin is very helpful.

This worked for us at Vimeo with the mobile apps. That way different files can be used, you just have to keep track of naming and versioning.

Would buy this for real