Right now all my stuff is custom so I don't charge extra (and I know I go a lot further for customers as far as custom stuff than most label sellers on Etsy).
I think the Pareto principle probably applies: 20% of your customers are 80% of the work :)
But when I was sewing, I did charge more for custom, just to cover the extra time for making the pattern or sourcing/ordering materials. Sometimes I was able to turn that custom pattern into a regular listing that I sold repeatedly, in which case I offered a discount to the customer for future orders, but generally it was a one-off.
I found more success with setting up a custom listing in my shop where there was a basic pattern but people could choose any fabric (100% cotton) on the internet that was less than a certain $ per yard (something like $10/yard); that way, you get custom orders, but you don't have to change the pattern or worry about crazy unexpected supplies costs.
You have a great shop that looks like it has a chance to really take off, so it's good to work out what you want to do about things like this beforehand.