As mentioned before, overlapping the pattern sections is the only real answer. But I like the stitch filter, that is mentioned in the faq, for patterns.
Ooohhh....actually I think that stitch filter was hosted a Open Clipart, which has been closed for some time. Or was it attached to the InkscapeForum post?? Well, if you can't seem to find it, let me know. I think I might have a copy.
No, there's no real hope of a permanent fix for it. It's just the nature of graphics, unfortunately.
I realize you're following up on this pre-existing topic here. But I just want to make sure you're aware of the new forum, in case you might have new questions someday.
https://inkscape.org/forums/ There's a message in red text on the forum index page, but apparently not everyone can see it. This forum will have to be shut down, in maybe something like 6 months to a year from now. I'll post more definite info when I have it.