I agree that the initial letter looks like an “E” and I certainly didn't take the word as “Täufer” when I first saw it---but then I am not very good at deciphering the old handwriting and always have to get hhg to help me. But when I saw that Renato had suggested “Täufer” it made sense, and I remembered seeing other initial “Ts” written in that stylized fashion.Zimmermann was well known as Anabaptist at that point. But I don't see the word after his name as Teuffer.
I notice that there is quite a large gap between the birth of the twins in 1687 and the baptism of Johannes at Schwarzenegg in 1695. I wonder whether there were additional children that Christian Zimmermann managed to prevent from being baptized? It is even possible that Christian was not present at the baptism of his son in 1695, and that it was done without his consent, or perhaps with his tacit consent. In the Sigriswil KB I have seen several examples of children of Anabaptist parents being presented for baptism by other relatives, I am guessing with the tacit consent of one or both parents. As the 1690s were a repressive time for Anabaptists in that area, perhaps Christian Z. was in hiding or had temporarily left the country?
The use of "Herr" and "Frau" for the two witnesses is unusual but I wouldn't (personally) take it as indicating high social status. Perhaps the witnesses were strangers to the parson and he was just being respectful? The Steffisburg KBs contain, as I am sure you know, many Wertmüllers.