When you think of the term modify it can make a lot of people cringe, after all, you are changing something that the manufacturer thought was a good enough design to sell it. I believe that this is part of what makes building rc airplanes so much fun. In fact, I purposely modify a lot of components to fit the way that I believe they should be.
There is a lot of times when I have disagreed with the plans and instructions that come with a balsa kit, maybe that is why some guys like to scratch build and have complete control over the whole thing (maybe it’s a control issue, probably should get that checked 
).
Seriously though, don’t think that there is one way to build a rc plane, I believe in questioning the process and seeing if there is a better way to do it, such as countersinking the holes of a mounting plate for retractable landing gear. Look at my picture below (and video) to get a better idea of what I am talking about.
Watch the video to see an in depth explanation and drilling demonstration in action. This is how I modify landing gear (maybe it is a simple modification, but its the little stuff that makes a big difference in the end when it comes to building rc planes).