Building question...
 

Is it bad form for you, a frame builder (I am not) to basically copy a bike's geometry?

Let's say I really like the geometry of the Surly Long Haul Trucker but I want it in Reynolds 631 or 853. Would that be an issue for a builder?

Second question. Hoping you are familiar with this bike above. How would lowering the top tube on the seat tube (so that it is slanted down) effect the bike? (Keeping the rest of the bike exactly the same. How would this change the ride?

In case you are not familiar...
http://www.tandems-recumbents.com/images/surly-lht.jpg

Well it isn't as though it is an original design or anything... There are probably a lot of makers who would blanch at not having the opportunity to take on improving your relationship to the frame. What is the basis for assuming the frame is right for you? There are some makers who do custom, but don't do buyer requests, they know what their bikes are going to look like, fitting aside. Most sports equipment that is made for the general market does not escape unscathed, and that is not a criticism. The average golfer should not have the same clubs a tour pro needs.

Lowering the top tube at the rear, the ride change depends on why it is being done. Is the rider in need of a frame for a person with shorter legs/arms ratio. I am 6 3 on the top and like 5 11 on the bottom, so a sloping tube gets me the stand over I need with the reach that fits me. But that would be a slightly different optimisation than the same exact frame with a lot of seatpost extension, for someone who will be riding in the third world and wants to dismount without ending up riding the rail, or for someone who wants an all square frame geometry, but wants to have a suspension seat post. It is the same frame, but each one departs in different ways from what would otherwise be that person's norm.

slanting the top tube more would have very little effect on the bike. If I told you it would be a little stiffer, would that make you happier?

Framebuilders "copy" geometry all the time. There are fairly tight limits on what works well on a road bike. Most people would still take your measurements and design off of those as a sanity check.

Not bad form at all...the LHT has a good middle of the road touring geometry. A custom builder could easily build you a bike that would handle the same, but would have the custom tweaks for a better fit.
Also, like it was said above, a sloping TT would have no real effect on the ride.