Just throwing my 2 cents in.
First, you will find very few vets that see teeny Chi's. Reason being is that the average Chi within standard is about 5/6 lbs. On average, 5 to 8 lbs. is the "norm." So their first reaction is usually to tell you that the pup will most likely have health issues that have kept the pup from thriving.
Pups are just like children. Until they reach maturity, a healthy pup will consistently gain weight. If they aren't, that's when you need to start thinking about blood panels, etc. On average, at Harpers size, you should see about 2 oz. gain each week. She could very well top out at 4 lbs. Runts develop slower. At full growth she may be Dad's size. The bigger pups may be following Mom's size. Usually the litter will be between Mom or Dad's size.
Genetic tinies aren't runts. They get their size from somewhere in their lines. Runts are many times just prematurely born with the rest of the litter. Being conceived from a later tie.
Tinies aren't common anywhere. You just don't see many that top out under 4 lbs. grown. Ethical breeders do not choose their lines for under this size for several reasons.
As for HW treatment, vets usually start that at 2 lbs. As none of the treatments are made for under this weight. With Jade, even though she weighs 2 lbs, my vet still recommends half of the pill. In a dog that size, you have to be very careful with meds. Even when healthy, it can be very taxing to their immune systems.
Your vet was smart to choose half doses of the vaccines. I almost lost Lexie to a horrible vaccine reaction. Her first vet was clueless, and so was I. Lexie being my first.
Most counties are very strict about rabies vaccines. But my vet is willing to take the liability going with half vaccines. It's really not even half that they use. But he's aware that a full dose could kill them. So it's great that you've found a vet that knows the risks and is willing to do the right thing by your pup.
My troop had their first rabies after their first birthday. But I know none of them weighed even close to 4 lbs. You might want to discuss that with your vet further. If your dog even nips someone without their rabies shot, they can force you to have them quarantined for 10 days.
The testicles are normally down by 18 weeks, but that doesn't mean that they won't drop. After 6 months old, it's safe to assume that they won't.
As Stella mentioned, a 5 lb. dog is tiny. Under 4 lbs., there isn't much to them. Especially the little cobby guys. So if little Harper makes it to 4 lbs., she'll still be itty bitty.
This is Chance at Harpers age. He now weighs right under 4 lbs. So there is a chance your Angel will hit some nice growth spurts. She appears very healthy for a wee tike.
Sounds like a great vet visit! Happy to hear all is well with both babies!