Being a doctor is , for the most part, being in a position of high esteem. So how did it come about that the verb to doctor ever took on the sense of to alter or falsify something for the purpose of deceiving?
I will pass on Merriam Webster's definition 1a - "an eminent theologian declared a sound expounder of doctrine by the Roman Catholic Church —called also doctor of the church"
However, if you have something wrong with you, you doctor it, a synonym for fixing it. If you buy frozen pizza, you are likely to doctor it by adding your favorite topping so it's somewhat palatable. (I don't doctor pizza, because I usually hate the crust, but I doctor other foods.)
Doctored documents aren't necessarily fraudulent. You're fixing whatever is wrong, but it may be that your intention is to remove an ambiguity and prevent a false impression. This is similar to "cooking" the data. When you conduct an experiment, you don't want to stop with raw data; you need to process it so that it can be consumed readily. The job of a bookkeeper is to process data in such a manner. An audit is done to ensure that the data was processed properly. If someone substitutes cooked data instead of raw data, instead of a nice vegetable stew, you end up with baby food. Yuck!
(Speaking of which, I baked butternut squash last night at 450F instead of 350F. With potatoes, 45 minutes at 450F, instead of an hour at 350F gives a fluffier potato and a crunchier crust. At the higher temperature, the squash retains a lot firmer texture, and develops a richer flavor. To think it took me half a century to learn a better way to make one of my favorite comfort foods!)