Rather than being a personal thing, it looks more like the quotes are estimates of the amount of time that it will take to do the work. When you cusomize the system files, any new customization has to ensure that the many customizations do not conflict and then program around those conflicts. I, too, have paid for customizations. But, I have studied the customizations that were done and kept the diff files. I take the responsibility to install upgrades on a local server, installed previous customizations from the diff files, and carefully tested. Then I can upload the entire upgraded and customized cart and database to my production server. Done that way, my only cost is the cost of the upgrade. There are no installation charges because I do the installation.
It gets frustrating that technology changes at an increasing rapid pace, but we aren't going to change that. With any cart, or software, you either buy something that is stock or you pay for custom programming. The disadvantage of custom programming is that as time goes on, it becomes difficult (expensive) to maintain and upgrade. There isn't a piece of software that I own where I don't wish it would or could do something that it doesn't. When that "wish list" gets too long and painful, I look for a replacement. But, over the years and many replacements later, I've learned that nothing does everything that I want. There is always something limiting me in some way. If nothing else, my needs and wants change as does my skill set and time constraints. I constantly have to weigh those wants and needs with the cost to achieve those.
When you made the decision four years ago, it was a good decision. But, four years is an eternity in technology. "Coulda, shoulda, woulda", is a no win exercise. All of us make mistakes. There isn't a person in business that wouldn't like a "do over". But, we have to deal with today, right now. You have to make the best decision for today and tomorrow, whatever that is.