I took a look at this, and it's not an issue of the Nakalim trait. Let me break down the different techs you brought up:

• Xenolinguistics, Eukaryotic Sap, and Botanical Scanning are Sophon-unique technologies, and as such receive the full bonus unless another sophon in the same match researches them
• Efficient Shield is a ship technology, which are exempt from the sophon bonus, as far as I know
• Off-World Agribusiness has a Horatio-variant, which is why it comes out as one less than you expected
• Plasma Metallurgy was displayed as 1 out of 6 when I tested the same setup myself.

Thank you. I did not know that the Sophon's OmniScience trait has the advantage of not counting someone if the opponent has a variant within the same Technology header or (vise versa) if the Sophon's have their own variant (unless there is another Sophon player to count towards it). That is surprising to me from its description, but I imagine it must be known amongst others who are accustomed to playing Sophons.

Here is my screen shot on mousing over the Plasma Meallurgy. It gave me the same (2 of 6) as before.

My game diagnostics: Diagnostics - 2019'09'18 @1107'41''.html

I tried it on a secondary computer I have, and it correctly shows (1 out of 6). So I'm not sure. It must be something on my end that I'm doing. I'll go ahead and tag this as resolved.

Speaking honestly, I think it may be a sde effect of the way variant technologies are implemented that just suited the affinity (because it helps you always get the bonus on Sophon-tech in games without other Sophon.) I admit the description is not necessarily clear about it, though.