Hello Matt,
Here is answer,
•Does Microsoft have access to message transcripts/logs?
-> I think Microsoft doesn’t have access to messages, they do not have access to customer tenant database were messages archives in exchange mailbox.
•Are connections decrypted and re-encrypted in transit?
I think. No.
•Is there an option for end-to-end encryption?
Yes, all Skype for Business/Lync communication by default encrypted.
Signaling information uses TLS
Media uses SRTP.
*Anyone from Microsoft can correct me, if i am wrong.
