The time is spent attempting to compile (I believe eventually with success) the last Table command because it has exceeded the default auto-compile length of 250. This involves, among other things, a full iteration over the table (I do not know all the details here).

Table can be dissuaded from doing this as below.

SetSystemOptions["CompileOptions"->"TableCompileLength"->Infinity];
a = Table[Random[], {1460}, {361}, {720}];

In[3]:= Table[a[[1, i, 1]], {i, 1, 100}]; // AbsoluteTiming

(* Out[3]= {0.000062, Null} *)

In[4]:= Table[a[[1, i, 1]], {i, 1, 361}]; // AbsoluteTiming

(* Out[4]= {0.000177, Null} *)

I will file a suggestion report that this handling be reconsidered with an eye toward optimizing it for better speed.

I don't know why the longer time, but this seems to be a workaround:

a[[1, 1 ;; 100, 1]]; // Timing
a[[1, All, 1]]; // Timing