Well, technically, the "standard" flanges aren't intended to restrict "your" design of "your" flange at all.
After all, "I" don't care what size and shape "your" flange wants to be, nor can I control how "your" flange is designed nor what service "your" flange will see. (And, since I don't know what your requirements are, I can't - and shouldn't - limit your needs. 8<)
But ... the standards aren't set up for YOUR desires (heck, they aren't set up for MY desires either!), they are set up so I can buy uniform, affordable flanges from any fabricator that will fit any other fabricator's flanges and fittings regardless of when the eqpt was built and who built the mating fitting, flange, or valve.
The standard sizes are made so the fabricators can produce flanges and fittings without fighting thousands of different sizes and spec's every time they get an order. At your end, if you need some odd configuration that needs to be specialty-cast, shipped to a forge shop, forged and thrown on a machine shop's lathe and specialty-turned for an hour or so to get what you need.... Then you need to decide how much extra time and extra cost that special design will involve.
If you can use standard sizes, then you can call up a standard supplier and get a standard size at a standard cost on a standard pallet on the back of a standard truck. Tomorrow afternoon. 8<)