You're certainly having much better results than I have :-)

On several cars over the years, having different types of paint finish
(colors, metallic vs. non, etc) I've never been able to do a scratch or
paint chip repair that looks quite right. Basically it comes down to this:
whenever I do ANYTHING to the touch-up paint after brushing it on, the
result looks worse.

My goal is a paint repair which is level with the original finish, has no
excess paint blob surrounding, and matches the original at least in color.
Perhaps I am expecting too much ... is this possible?

Normally I follow the suggested paint sequence: clean away rust and loose
paint to bare metal; apply a thin coat of primer, let dry; a thin coat of
paint, let dry; a thin coat of clear coat - assuming the defect is thick
enough to accept all three. If not, I just use paint.

Originally I sanded the pain blob down with microfine paper until it was
level and then polished. More recently I've used a product called "Langka"
(http://www.langka.com) which is a kind of polish/solvent that removes
excess touch-up paint but leaves the cured factory finish untouched.
This is very fast, can be done an hour after applying the paint, and
there is no damage from sanding. It is also a terrific way to recover from
"Oh, sh.t!!" such as what happens when a drop of paint drips from the
brush onto your car.

No matter what I do, and using several batches of paint from different
sources (factory, Dupli-Color, Plasti-Kote, etc) the painted defect ALWAYS
looks darker than the surrounding factory finish.

Issues I continue to run into:

1. You can never seem to apply touch-up paint with a brush in layers that
match the thickness of factory paint. So when you remove the "blob" to
level the repair with the original finish, you end up going so close to
the primer layer in your repair that it shows through and you have to
start again.

2. Metallic touch-up paint seems to layer when applied, so that only the
top surface is the correct color. When you sand or Langka away the top
layer, the exposed bottom portion is darker, has few metal flakes in the
pigment, and no longer matches.

3. Many recommend a layer of clear-coat if the original finish is of
that type. Why, then, does a brush-stroke of touch-up paint match
decently, but if I put a brush-stroke of clear coat it top it is now
darker the original finish?