If you can do 'real pull ups' go ahead and dont worry about lower round/times you will get better!! Log it to keep a record, I can see at least tiny progress in my log every week.
I am quite passionate about this point and I know what you mean. I was the same at the beggining and in some respects now still, but its not about the level you are on. I was round my bro's house with some friends and they go to the gym frequently and for years and supposedly advanced but their pull up form was BAD! Taking the time to level up when it was right for me has meant that my form and ability is far better for it.
I strictly did not level up until I could do L1 D3 all real pull ups and under 5 minutes (harsh reality is that those are the rules for this program). Like you say this was hard and I struggled for several months trying to get my first pull up then doing more etc etc. I am so glad I did not fool myself or my progression with levelling up with substitutions.
If you can't do pullups then try as hard as you can to do as many rounds as you can on day 1 and you will get better!
I advocate staying at level one to all those who cant do a pull up yet. The joy, feeling of success and progression when you get to level 2 is excellent!