How fast does arduino process each line of code?

A line of code is not directly executed. It is translated to machine langage by the compiler. So a line in your source code is translated in a certain amount of instructions and you can't predict exactly how long it takes for a line to execute.

But this is not a problem if you want to add some user interface.
When you are modifying parameters through some user interface (reading push-buttons, displaying informations on a LCD) you don't want the system to be has fast as when you take the snapshot.
The size of the program has no relation with the time it takes to execute one portion of it if that portion is well written.

If you want the part of your program that trig the flash really fast, you should be aware that in that part of your code no unnecessary instruction takes place.

You should cut your program in a "user interface management" part and an "operational" part. Only the operational part should be written with execution time efficiency in mind.