Are you thinking about seadeck on the deck or wrapping seadeck around the toe rails? If the first case, seadeck applied to deck, if you want to make more space, you might want to trim the lower edge as mentioned but not the sections where the screws are. I wouldn't remove more than 1/4 inch, maybe a tad more. The edges if like mine are routed to give a roundover with a edge profile. Anyone with woodwroking experience would understand what I am talking about, a roundover bottom bearing pattern bit. You will also need to make a template and temporarily screw it to the back of the rails for the pattern bit to follow.To do the job correctly, the rail will have to be removed. Be aware that the older the rail, the more likely it will be to have stress cracks near the mounting screws from expansion and contraction. Those cracks will often result is pieces breaking off.
I have found the following tips to be helpful when reinstalling the toe rail:
If you have three sets of screws, two ends and one middle, leave the middle screw holes as is but redrill the end holes one size bit wider. I also try to make the hole a bit elongated. That allows the rail to expand and contract without undue pressure on the screws. Do not overtighten the end screws or the middle screws for that mater.
Secondly, over time the rail may expand a bit and rub up against the walls of the deck mold putting extra pressure on the rail. f that happens, the rail will start to look wavy or bowed. That will be more obvious in the hot weather than the colder. If the rail does not have end clearance, the tight ends should be filed or trimmed to add clearance.