Anytime you take a standard plan and personalize it (by selecting a date, etc.) & then either optimizing/evaluating the order, yes it will take into account the data it has for wait times for the expected crowd levels. Absolutely it takes into account the closures (that TP knows about) & showtimes. However, crowd levels are consistently higher so make sure to pad your plan with lots of "buffer time" Inserting breaks every few hours is a good way to manually pad your time, plus you will be using that time to stop & eat and also probably for pit stops to hydrate, apply sunscreen, use restroom etc. I also like to set the walking pace to relaxed or very relaxed to account for my family's already more meandering pace & allow for time to stop and take in the spontaneous magic that is a part of Disneyland's charm.
Because Disneyland is so "subject to change" when I do a plan in advance, it's always best to re-visit it whenever I have time the week leading up to the trip (sometimes on the way there!). I like to double check off the Disney website for anything that's super important and then when I am really on my game, once I arrive at the parks, I compare my plan with a printed times guide to make sure showtimes match.