LOL, good idea to just get around those pins if you don't need them. Why didn't I think about skipping those pins? Many of my early projects using thru-hole parts, like doing two photo gates etc only needed a few pins. A 1/8" stereo socket fits on a perf board just fine, so is a thru-hole power barrel with pins. 0.1" and 0.2" spacing screw terminal blocks fit too. I've even fit coin battery holders and buzzers on them, although I had to use different rows of pins.
But to be honest, there is no way I'm going back making perf board projects. My right hand is glued to my mouse now. Sometimes I just make a design and get it printed and THEN prototype it on the PCB. Printing gets so cheap that if I make mistakes, I keep the coasters in a pile as practice material for my students.