My question is...is it OK to rough in the water supply to the toilet on the right side , to hide it in the corner of the bathroom even though the hook up is on the left side?
You can put it where you want, but you might have trouble finding a supply hose long enough. If it's placed optimally, often it's very hard to see on the 'normal' side while still being accessable when needed.
Forgive me for asking, it's really none of my business, but why are worried that the water supply to the toilet might be visible? Everyone has a toilet and I know of no one that tried to hide the supply line. Put it on the left side as you face the toilet where it belongs. Use a chrome cover around the pipe and a nice chrome 1/4 turn valve with a flex supply line of appropriate length.
I know... trying to build my own house and trying to make sure everything is almost perfect...don't want any " wish I had done that diferrent" situations.
If you don't like the look of the flexible supply hoses, you could always plumb it with chrome (or whatever finish) plated brass solid line - this is thinner and potentially 'neater' looking than a flexible supply line. that takes more skill and maybe a tubing bender to get the things to line up without kinking the tubing, but those are cheap (takes more skill and time, though).