On the left is a GT28RS (disco potato , keep in mind this turbocharger has a internal wastegate (actuator) ) on the right is a stock s13 sr20det t25 turbocharger. Both are pretty much the same size. I believe the RB25 turbo is a T3 flanged turbocharger , so to get a true bolt in replacement/upgrade for your setup i'd go with a GT28RS t3 flanged turbine , but you would end up having to go with a external wastegate (something i'am sure CMS can do for you). But either way you shouldn't have clearence issues.

Edit: By the way these pictures are from sportcompactcar's website, courtesy of their project silvia.