I'm a little confused interpreting the statement of the classification of covering spaces in Hatcher's text.
Let $X$ be path connected, locally path connected, and semi locally simply connected. Then there is a bijection between the base point preserving isomorphism classes of path-connected covering spaces $p:(\tilde{X},\tilde{x_0})\to (X,x_0)$ and the set of subgroups of $\pi_1(X,x_0)$. If basepoints are ignored, the correspondence gives a bijection between the isomorphism classes of path connected covering spaces and conjugacy classes of subgroups of $\pi_1(X,x_0)$.
The way I'm reading "the base point preserving isomorphism classes of path-connected covering spaces" is that you fix a base point $x_1$ in the covering space $p_1:(X_1,x_1)\to (X,x_0)$. We identify $Q(X_1,x_1)$ as the collection of all covering spaces $p_2:(X_2,x_2)\to (X,x_0)$ where there is a homeomorphism $f:X_1\to X_2$ where $p_1=p_2\circ f$. Then for each subgroup of $\pi_1(X,x_0)$, there is a corresponding $Q(X_1,x_1)$. But when he talks about ignoring the base point, does he mean now that if we keeps $X_1$ the same, but change $x_1$ to $x_1'$, then $Q(X_1,x_1)$ and $Q(X_1,x_1')$ correspond to conjugate subgroups of $\pi_1(X,x_0)$? Is it not possible that $(X_1,x_1')\in Q(X_1,x_1)$?