When the updater checks what to update, it always and only compares the local Modpack folders with those in the server, right? It won't check whether the local non-Modpack folders(e.g. MyMods) have mods that shared the same GUID or not. You see, players can have newer version of the mods that are listed in Modpack in their local non-Modpack folders.
The updater doesn't allow players to deselect certain mods when they try to update a Sideloader Modpack, nor does it ignore the mods that have newer version in local. In this situation, the updater will download the duplicate and older version of mods, and the users can't simply reject it because the Siderloader Modpack could contain things that does need to be update.
So I suggest adding feature to allow users to select or deselect specific mods to update in the update check window, so we can decide what to update on mod base instead of on Modpack base.
Alternatively, the updater could do its check based on GUID&mod version number of all local mods so that it only lists the newer and non-duplicate mods for users.