I recently went through this process for a fairly large database (~30000 scripts). I found the SSMS wizard cumbersome, as you point out, so I didn't want to repeat the experience for each class of entity. I scripted everything into a single folder, and used a series of MOVE commands at the command prompt:
move *.table.sql \tables\
move *.storedProcedure.sql \storedProcedures\
etcetera. I found this faster than the recommended approach, and more amenable to scripting (if necessary).
I am not sure I understand the recommendation to alter an entity in SSMS and then rescript all entities of the same type. Once the entities are scripted, is it not wiser to only edit the scripts? I find that allowing people to change entities in Object Explorer is a recipe for disaster, as they inevitably forget to update the script (and in large databases, rescripting everything to capture one change is costly). Do you automate your scripting to occur every night? That would make more sense from an overhead perspective, but you might lose auditability....
I'll go back an re-read, I might have missed an important note or two.