How to generate Assembly drawing with designators inside the boxes like this in Altium? Is it by placing designators (silkscreens) inside manually? I guess not.
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It can be somewhat automated, but it is tedious to do the first time, because you have to modify all your footprints
What I do is
Altium will automatically replace the ".Designator" text with the actual designator when you generate output.
There are some helpful Altium scripts for centering and sizing ref designators that can be used for your purposes.
Lots of useful scripts live in here (this used to be a project on google code):
These two can center and resize ref designators according to the component outline size:
And this one can move ref designators onto designated mechanical layer pairs:
These are also a good starting point to write your own script if you want to customize the behavior further.