Are lap or slip joints directional.

Does it matter which way they go when building a custom exhaust? I'm going to weld them anyway. It would be easier for my the first bend to slip up into the head pipe off the manifold but, that seems backwards. The exhaust flow would be hitting the end of Each pipe downstream, if that makes sense. I could butt or flare one end but, more trouble.

You would be restricting area by slipping inside the head pipe. Always downstream overlaps or butts to upstream.

In "theory " yes. Next pipe down the line should be on outside of previous pipe.
But consider this..
Is there any restriction ( hood, grille etc) for air getting into your air inlet ?
Is there any restriction for air getting to the air filter ?
Is there any restriction for air getting to the carb , throttle body, injectors, etc ?
Is there any restriction for air/ fuel getting into the head ?
Is there any restriction for air/ fuel getting past the intake valve ?
Is there any restriction for the exhaust getting past the exhaust valve?
Is there any restriction in the exhaust gasses getting into the exhaust manifold / headers ?
Are there any tight bends in the rest of the system or reducers going into or out of the mufflers ?
Some of what goes in, has gotta come out. If not, there would be no "exhaust"
Most any welded seam exhaust tubing (except "seamless" ) l have ever dealt with has excess weld inside the entire length which, guess what, is a "restriction "

You MAY have a couple of other things to consider than if a couple of joints ain't exactly " correct ".
You could always grind / bevel / taper the "inside of the inside" pipe to create a smoother flow, l suppose.............
I wouldn't worry too much about a couple " wrong way" joints unless everything else is "perfect ".

Think of what happens to the coolant in your engine.
It comes upon a "inside" lap joint every time it goes into the radiator from the upper radiator hose.
It comes upon a LARGER "inside " lap joint everytime it goes into the water pump from the lower hose.
Not many people try and "smooth out the flow" there.
(Except maybe the racers l associate with)