Modern translations of medieval texts frequently translate the Latin verb 'sit' as he/she/it is. However, 'sit' is the subjunctive mood of the verb 'sum'. In my view it should be translated as he/she/it be as in: "Videtur quod pater non sit in filio ..." which is frequently translated as "It seems the father is not in the son." Instead I prefer "It seems the father be not in the son." Comments please.
The trick is the context.
In this case, you have a subordinate clause with videtur "it seems" and quod "that". This is mostly a mediaeval-Latin construction; in Classical prose I would expect ut or an accusative-plus-infinitive instead.
But in mediaeval Latin, videtur quod generally takes the subjunctive. See this answer by brianpck (and the question itself) for some further analysis. In particular:
The moment we depart from such words and move on to verbs like cogito and (especially in medieval Latin!) videtur, the subjunctive predominates.
On a philosophical level, you could say that the subjunctive is because "it seems" to be a certain way, it isn't necessarily fact. But linguistically, it's easiest just to say "this is a construction that puts its verb in the subjunctive".
In English, on the other hand, the subjunctive is nearly extinct and very rarely used. The English impersonal "seems" always takes an indicative: "it seems like he wasn't here", not *"it seems like he weren't here" or *"it seems like he be not here".
So in this case, I would say "it seems that the Father is not in the Son" without reservation. A phrasing like *"the Father be not in the Son" just sounds somewhere between archaic and ungrammatical to my Modern English ear.