Now after opening both machines it seems pretty clear that my 512k is an upgraded one.

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It was always clear to us! LOL No 512K ever had a SCSI port.

One thing is still a bit strange: while my Plus shows all the signatures on the inside of the beige backside housing the "upgraded" backside housing from my 512k is missing these signatures and is held in black, it also misses any further engravings that my Plus shows but it is definetly a housing from Apple.

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Not sure what you mean by "misses any further engravings".

As for the signatures, they persisted in some form through the SE/30. So for a beige Plus kit not to have them is quite odd. When you say "held in black", so you mean the metallic RF coating on the inside of the case is "black"? If so, I have seen compacts where the shielding coat is so thick it conceals the signatures, but if you look real closely you can still make out a few. I suppose the Plus case backs could have been manufactured at some of Apple's new international plants and as such used a new mold that did not have the signatures, though I have never heard of this.

I think I will exchange the mainboards. My Plus has 4 MB RAM, the 512k/Plus just 1 MB. The Plus also faces the video dropouts which the 512k doesn´t show. So when I´m reanimating my old Plus webserver the 512k will be a bit more "special" for this job, I suppose

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If you are planning on using the 512K as a server, consider that the 512K analogue board is not as robust as the Plus board and therefore is subject to burning out faster, especially when left on continuously. You are better off repairing the Plus board and switching it to the 512K case if you prefer its design.