"Shall not" seems harsh to me. If an organization wants to make something, run it entirely through QA/QC to accept the final configuration (possibly including paint or plating or assembling to a bunch of other parts)n and put it into a little cardboard box with a label on it - and then take it out of box, throw the box away, and then send the item right back to the machine shop to risk other damages, then they should be allowed to screw themselves over.
It also messes with ERP - the altered item drawing shows the company buying one item to be altered, but to make that item the company has to procure raw materials, maybe do some welding, some machining, maybe some plating and painting, then off to inspection with the components, possibly then to assembly and another inspection - none of this will readily show up in the ERP system unless someone says "Hey, that's our own part." And then, as mentioned before, that only gets them to the starting point for altering the item. It buries costs as the sales price of the item isn't the correct one for altering it like it is for items coming from outside the company.
Oh - if a customer breaks an altered component of an assembly, this can mean they cannot buy a replacement part - the alteration is at the assembly level, not the component level, Some makers do this and it's really annoying - can't replace a $5 pollution control valve - it's integrated into the $1500 intake manifold. There's a potential to force that by using altered item drawings incorrectly.
It's almost always better to just create a new version of the thing, re-use whatever sub-assemblies one can, and fold in the appropriate new parts.