A Snarkling's comment plucked from the comment roll at "To Dream the Impossible Dream":
Here is a related question to your statement, "I don't send form rejection letters to people I think just need a bit of reworking. Those folks get specific letters and suggestions." I once received just such a letter from a top agent -- lovely letterhead, personal signature, the works. The advice was invaluable, but it did not include an actual suggestion to "resubmit at some point."
So, when YOU send a personal letter of this nature, do you have expectations? Do you specifically ask to see something "later?" Or might you be "testing" the writer to see if she's up to snuff? The agent who honored me with this kind of personal response went so far as to express "frustration" at having to pass my work by. What does that say to you? What should it say to me?(For me, it ultimately led to serious revisions resulting in a better work.)
When I send a letter that says something other than "not right for us" the only subliminal message is "you're writing something that I recognize as closer to what I'm looking for than the usual stuff". It's not a test. It's also not an invitation to resubmit. It's encouragement to do exactly what you did: revise and get better.
After you've done that, then you query again.
The biggest problem I've found with people getting these kinds of letter is that they redraft, and resend at the speed of light. You'd think they had Mr. Scott running their damn mail room. Even when I specifically say to sit on the manuscript for a month, I've got another query on my desk in 31 days. I can't over emphasize the power of letting time pass and looking at something after it's had time to cool. Writing is not a soufflé. You can quote me.
The other thing to know is I don't keep track of those letters very long. Maybe a couple months just in case. I have enough stuff to track without worrying about the query letter/slush pile.
If I want someone to resubmit, I say so. I try not to make it a game of "will she figure out what I want". Clear communication is hard enough without trying to be clever. I assume most agents operate the same way, but truthfully I've never inquired.