Autocrypt - allways added to headers

A big point of Autocrypt is that you distribute your public key with every email that you send. See also https://autocrypt.org/

What do you mean by “header sections going to[o] long”? There’s no size limit for email headers.
Are you maybe running into this issue: Use folding to properly handle To/CC/BCC with more than 1000 characters? In that case please update to the latest beta version.