I just found this thread after trying to do the exact same thing, very interesting.
I also don’t like having to do all my Inter account transfers manually and must agree that there is reason for this request from me also. Had 20 to do already this month and more will follow as businesses increases. I can understand both sides of this but believe the speed this feature would add to inputting transactions would be invaluable to me personally. As long as the end user understands double entry then they should not get themselves into any situations using this feature.
An example, I transfer many times from PayPal to my main bank account and this is always done instantly so no worries on my side regarding dates etc. If this feature was available i could import PayPal statement and assign all the inter transfers via the rule suggested and then just delete all of the transfers from the main bank CSV before import and i would be done 
No double transactions to worry about. It would be so simple and as its always the same kind of transfer, a bank rule to do this would be a really great feature. I understand it would not suit everyone but it would save lots of people hours of valuable time.
At present i just reference all the transaction in the PayPal CSV sequentially, make note of dates, amounts and references of my inter transfers and then delete them from the CSV and enter them manually after finishing the import. When doing Bank CSV i only take note of the reference i want and delete all the transfers before importing. This seems to be the quickest way i can figure to do this but i have only been using Manager for a little over a year so still learning