Rabbi Meir does allows witnesses to write a shtar even if they do not recognize the parties, but the shtar cannot be collected without corroberating evidence because he is afraid that a bet din to'yim will rely on the witnesses. And the Tur decides according to R. Meir.( See HM 255:1) And yet the Tur also decides according to R. Dimi of Nehardeai that the halakhah is ein hosheshim lebet din toy'im ( See HM 46:8)!??
We don't Pasken like Rebbi Meir, but rather like Rav Huna's version of the Beraisa that the Chachamim say we write the Shtar because we are not Choshesh for a Beis Din To'im. Though the Beraisa originally quotes this opinion in the name of Rebbi Meir, the Gemara later which says that Rebbi Meir is Choshesh for Beis Din To'im is according to Rav Huna's version of the Beraisa that Rebbi Meir says not to write the Shtar at all because he is Choshesh for Beis Din To'im (see Shach C.M. 39:36 who clearly states that in both of the above Simanim we are not choshesh for a Beis Din who are To'im).
All the best,