Amazing, Absolutely Amazing.
This is a great bug find. Yes, This is actually a bug.
After investigating this issue more closely it looks like the option "only resume files transferred in binary mode" wasn't being applied for site to site transfers at all. I double, triple checked and I couldn't seem to find anything, I have added the missing support and I'm in the process of testing it out.
In addition to this missing feature I also discovered a mistake in the File Exists Option dialog, Apparently the per-site option is saving its value to the wrong place, I corrected this mistake.
Both of these issues will be resolved in the next build.
Thank you so much for reporting this issue.