How long should it take to read a paper?
As you have alluded to, there are many ways to "read" a paper and the first question to straighten out is for what type of information are you reading a specific paper. A beginner's mistake is to believe you need to read from the first to the last letter of everything you find. This way you never get anywhere and it is the beginning of the learning curve for undergraduates.

If you are surveying a field, you skim through by reading the titles first of all just to spot the ones of interest. This reading takes much less time than to actually find the title. Once you are past this you may take on the abstracts to weed out the ones that sounded right but were off topic. This will take a few minutes per paper. The next step is to read the parts that are of interest to you. Are your summarizing a field then conclusions and the discussion may be what you focus on. Maybe your summarizing methodology then those chapters are of interest. In any case, you will read parts of the paper that are mostly relevant to what you are trying to find out. This may take a on the order of hours, sometimes less per paper.

Sometimes you need to spend time on papers to understand the nitty gritty details. I spent 4 days reading three papers to understand the details. I needed to write down equations and try to see the missing steps between the paper equations to understand the derivations etc. This type of reading is not what you normally do but it certainly happens.

So in the end, what you will learn through your PhD is to hone your skills to be able to focus on the details you really need from any paper. It is rare that one reads one paper at a time, usually it is a collection of papers and one often has to return to check on details that you either have forgotten, or may have missed, or, in fact, the author has missed. The need to go into the smallest detail of a paper depends on what you need to get out of the paper and with time (continuing through your professional life) you will improve on these skills through additional reading.