Copied spells and the two free spells are separate
Note the full wording1 of the Learning Spells of 1st Level and Higher section (emphasis mine):
Each time you gain a wizard level, you can add two wizard spells of your choice to your spellbook for free. Each of these spells must be of a level for which you have spell slots, as shown on the Wizard table. On your adventures, you might find other spells that you can add to your spellbook (see the “Your Spellbook” sidebar).
There is a clear distinction here. Whenever you gain a level, you get two free spells. Separately, you might add other spells to your spellbook, as detailed in the spellbook sidebar. These are two separate methods of getting additional spells for your spellbook.
So if you have scrolls or another spellbook, you can copy any of those spells following the costly copying method, independently from the free spells obtained at level up.
1. Apparently some older versions of the PHB did not have "for free" at the end of the first sentence of the quote. It seems to have been added silently (without being noted in the errata docs), according to Someone_Evil.