First, a disclaimer: I've only tested this in the current Snappy Ubuntu Core edge-- not on the desktop.
I believe the version of the snap in this situation is actually irrelevant-- the important part here is the developer/publisher of the snap as far as the store (and snappy) is concerned. The snap coming from the store is associated with a specific publisher (e.g. your store account), whereas the one being sideloaded isn't (or maybe you could say it's associated with the "sideloaded" publisher, heh). This is reflected in the Developer column of snap list.
If you sideload snap "foo," and a snap by the same name is also in the store, the one you sideloaded is considered a different package and I believe it will not update automatically-- you'll have to install the one published in the store (note that you'll first have to uninstall the sideloaded one since they have the same name). However, if you install snap "foo" from the store and then sideload another snap "foo" over the top of it, it'll treat it as a new version and you'll notice snap list says it's now sideloaded. I expect this means it'll no longer update from the store.
Note that if you sideload the same version as the snap you installed from the store, it seems that the store version is overwritten.