Early rifles, Lee-Metfords and the first variants of the Lee-Enfield, had no charger guides. The magazine was loaded by hand and was intended to be held in reserve, and only used by order of an officer. Otherwise, the rifles were intended to be singly loaded. The spare magazine was intended to be a replacement for a damaged one or, in extreme circumstances, used if there wasn't time to reload the primary.
The first Lee-Enfield to incorporate an integral charger guide was the Mk I, adopted in 1902, although some Pattern 1895 (Magazine, Lee-Enfield) rifles were retrofitted with charger guides based on experience in the Boer War.
Even so, the loaded magazine was still to be held in reserve and the rifle single loaded.
The loop on the magazine was a keeper. Its original purpose was if the second magazine had to be used.
Once the second magazine was dropped with the advent of charger loading, the keeper was retained to make sure that the magazine wasn't inadvertently lost. Replacing a lost magazine could be something of a pain in the ass when you're half-way around the world.
I believe the keeper was finally discarded during World War I, when a lot of frills and non-essentials (magazine cutoff, volley sights) were dropped to speed production.