I just took a look at your Album, and unless someone has grown a lot since the last pictures, I do not get it. I can't figure why a vet would say it if it were not true unless he was on a "kick." I have even seen human doctors get overly focused on one thing and try to over-diagnose it. I had it happen to me. AFter getting a questionable dx, I read a column he wrote for the local newspaper on just the problem he told me I had. I changed docs and found I did not have the problem he dx'd. So, if you believe their weights are appropriate to their body structure, I might seek advice from another vet.
But, if they might be a little overweight, remember "obese" is just a word associated with a certain percentage over the recommended body weight. So, if they might be overweight, please try to take the doctor's advice -- but maybe ease into it. Try starting them with twice a day feedings for a while to see if that would help (run it by the vet as a valid compromise). Also cut out treats and any between-meal extras. They might not eat much at a time to start, but they will eventually get hungry and eat more at a feeding. I do feel twice a day is as few feedings as I would want to go with for a Yorkie.
Like you, I like to free feed, especially with toy dogs. Mine are free-fed but are described as "lean" by our vet. I always worry they are too skinny, but he assures me this is the healthiest weight for them and will add years to their life. So, if yours do need to lose a little, keep in mind that it will keep them with you longer.
Good luck with those cuties!
I just realized I had already responded to this thread last month!
I should really start reading all the way through before making a post!