One more factor to consider is time. If you have all the parts already on hand and want to make it now you will probably choose the protoboard. But if you will

One more factor to consider is time. If you have all the parts already on hand and want to make it now you will probably choose the protoboard. But if you will have wait a week for parts to arrive anyway and the cost of board (for the specific project) is negligible might as well order the pcb in parallel. For a simple board that you could do on protoboard, the layout process on a computer shouldn't take much effort either. The comment about more easily mounting certain parts applies not only to SMD parts, but can also apply through hole components. You protoboard will probably have 0.1 inch spacing between holes, just like most DIP ic packages, and you can bend resistors and capacitor legs however you want. But there are occasionally some through hole components like buttons, switches or specialized connectors which might have a different requirements. Trying to workaround those can result in a bit janky result. And if you are making something practical you want to use daily, having something more robust and less janky can be nice even for a one off project. At the end of day it's one more tool in your toolbox. And different people make different kind of hobby project with different needs. I recommend you to try doing it a few times so that you are familiar with the process and overcome the stage where you avoid it just because you have never done it. Afterwards for your future projects you can choose the method that's best suited for specific project. Being familiar with more tools can also open you doors to new projects that you wouldn't try otherwise.