As long as the chain runs true to the windlass from the stopper and you have the stopper properly mounted (sounds like you do) you should be good to go. I'm not sure I understand your concern about when the anchor enters the roller? As long as you have enough length between the stopper and the end of the shank when it's pulled in tight there shouldn't be a problem. The chain will make it's "bend" at the stopper instead of at the windlass, but I've always figured that was good for the windlass. Make sure your backing plate is as large as physically possible under the mounting location.
SV Laurie Anne
1988 Brewer 40 Pilothouse