I am trying to understand the proof of the following theorem (from the book: Homotopical Topology by Fomenko & Fuchs):
Before this theorem the book only talks about paths. Couldn't it be a loop $\alpha:I \rightarrow X$ such that the lift of $\alpha$ is only a path (not a loop)? Is this why this map is not an isomorphism? Could we have a loop $\beta: I \rightarrow T$ that is not a lift of any loop in $X$? Really would appreciate help here.

You’re correct that the lift of a loop is in general a path, so that the given map is not necessarily an isomorphism.
The image of any path (i.e. an image of some map from $[0,1]$) under the covering map is again a path, and if the path is a loop (i.e. its endpoints are the same point) then the image of this loop under the covering map is again a loop.