I am aware there is a question similar to mine here and here, however I'm asking because I have a more specific question regarding this issue. Some explanations I've gotten as to why we use combination is that the order doesn't matter. HTHT and HHTT is the same number of heads. But then wouldn't this mean that the "number" of ways we get two heads is just one? Obviously not because ${4\choose2}$ is not 1.
Furthermore, can someone explain what $\frac{n!}{(n-k)!}$ would mean in the context of the "4 trials, 2 heads" example? In permutations since order matters, doesn't this mean we count HHTT, HTHT, HTTH, and so on? But then when I add this up this comes to a total of 6, which is actually ${4\choose2}$!
Your confusion is on the meaning of "the order doesn't matter".
When we say that there are $4\choose 2$ ways to get two tails in 4 coin flips, it's because there are $HHTT, HTHT, HTTH,$ etc. There is a first coin flip, a second coin flip etc. and in this respect, the order matters as $HT$ is not considered the same as $TH$.
However, to count the amount of ways to get $2$ tails in $4$ flips, we count the number of ways to choose $2$ placeholders from a total of $4$ possible options. To get $TTHH$, we choose the first two placeholders. And here is where the order doesn't matter: if you choose the first placeholder, and then you choose the second, or if you choose the second and then the first, in the end you get $TTHH$. In other words you don't even have to choose them one by one, you can choose your two placeholders at once.