Encoding the stream myself using Base64Encode and flags set to 1 fixed my problem.

There is no CRLF anymore in my stream.

Here is my final solution (error handle ommited)

s stream=##class(%FileBinaryStream).%New()
s stream.Filename = filename
s encodedStream = ##class(%GlobalBinaryStream).%New()
while ('stream.AtEnd) {
      d encodedStream.Write(##class(%SYSTEM.Encryption).Base64Encode(stream.Read(12000),1))
}
s propertyPath = "PIDgrpgrp(1).ORCgrp(1).OBXgrp(1).OBX:5(1)"
s seg=target.GetMutableSegmentAt($P(propertyPath,":",1),.tSC)
s tSC = seg.StoreFieldStreamRaw(.encodedStream,$P(propertyPath,":",2))

Thanks Armin for your help.