Syncthing encrypts the data, so it will be encrypted when being transferred. However, Aegis can export the vault into an encrypted file, too. So the vault file you will be transferring over an encrypted channel is encrypted itself as well. That means that the vault is secure even when at rest on some device.
As a researcher, I am very happy that recently all the conferences and journals we usually publish to champion open access publishing. Due to this, all my work is currently FOSS and all the papers open access. That is a great change to the papers of the past where you have to have an affiliation to a university to get access to a paper and sometimes even that is not enough.