Thanks for giving Yummy a try, and welcome!

Since I'm already dealing with your modification date issue via email support, I'll post the result of my suggested fix here when you have confirmed it. If I am correct, the solution is to enable the 'Validate suspect file datestamps' checkbox in the Server Options tab of the Preferences. This is a known issue and is fixed already in a new build which will be released shortly.
The Bookmarks in a side drawer is already being worked on. I hope to include it in the update after next.
The disconnect functionality is indeed different to Transmit as you noted, in that once you disconnect you are presented with input boxes to make a new connection. With Yummy, you can leave the server as-is until you need it - then it will automatically reconnect. So, for example, you could drag files to a folder in the server listing while it is disconnected and Yummy will re-connect and then upload to that folder.
Thanks for the wonderful compliments! I'm working hard to provide everything I can

-Jason