If you are drafting by hand, it is time consuming to remove the seam allowances. Pattern blocks are made with seam allowances on. You would have to keep a set of blocks without seam allowances. It would be so easy to mix up seamed and unseamed pattern blocks. Apparel pattern makers leave their blocks seamed and theatre pattern makers leave their blocks (or rather slopers) unseamed. In fact a block is a finished pattern piece that includes all pattern markings and is seamed.
If you are drafting in CAD, you can turn the seam allowances on and off. You can work on the cutting line or the stitching line. It's a simple matter of hitting a few buttons. BUT, I have found that CAD programs have difficulty in calculating between seamed and unseamed because it involves a complex series of mathematics. So constantly switching between cutting and stitching lines can produce some weird anomalies. (As an aside, weird things can happen with notches on stitching versus cutting too). I have found this is true no matter which CAD system you use. So I work with seam allowances on and directly on the cutting line nearly 99% of the time too. This means that I keep the seam allowances in mind while I work.
In CAD, it is important to turn the seam allowances off and walk the pattern pieces along the stitching line in a few areas. Collars and necklines is one area that I nearly always check for matching on the stitching line. There are other situations that come up where this important. I learned this the hard way recently.
In this situation, I split a jacket back pattern piece and added corresponding seam allowances along the split line.
Next, I aligned the pattern pieces to make sure the match. At this point they did and I assumed all was right. Until I got complaints from the sewers that things weren't matching up. I had to go back and double check.
I took the seam allowances off the pattern pieces and realigned them. They didn't match, so I redrew the stitching line of the side piece to make sure it matched the center. I added back the seam allowances and realigned the edges.
The pieces didn't match again. Sewers don't like this usually. In this particular case, the seam allowances are small, so I left the little "dog-ear". It can be difficult to cut those "dog-ears" off by hand when they are really small. It is easier to machine cut. In any event, there are different ways of dealing with this. I show one method below.
Your pattern pieces will then look like this and match up in every way possible.