Can the silkscreen be placed inside the footprint for the through-hole PCB? This placement might help reduce “visual congestion.” What are the problems associated with it?
Silkscreens are a “feature” and not a necessity. When a board has lots of empty space it’s really nice to have large, readable , reference designators right next to the component and in the same axis. When the board becomes extremely dense, you leave them off altogether and create a document to illustrate them. In between those two limits, you do what works.
The biggest drawback to not having them all easily visible is that it makes it harder to troubleshoot when something is wrong. It rarely affects the assembly stage because they have pick-and-place files, plus files for what ever layer you ended up using for them, plus “machine intelligence” that knows where C43 is and will take you there.
Since it doesn’t sound like you have to hide all of them, just make the text as small as practical (e.g. 0.030” height) and hide the ones you need to. Having them hiding there on the board is better than not having them at all.
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The legend can go anywhere you want it. Only issue is having it hit pads but this can usually be identified and corrected at the CAM stage.
Silk is useful to mfg techs and of less benefit after final assembly. Note that as SM packages get smaller, too much silkscreen can afffect solder paste application and reduce ability to clean under components if that is something that you are concerned with.
So yes you can add silk inside component footprints but that silk will only be visible until the component is placed - which reduces reasons why one might consider that. I recommend avoiding that unless you have a really good reason to do so.
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