I have run into similar issues with some cemeteries I have added. I don't use the name of town unless it lies within that town's boarders. I always use the Township or District in which it sits.
For Example: In my home county of Hancock in West Virginia is the Cemetery known as Locust Hill Cemetery. It serves the community of Chester and the northern area of this county (for the most part). Locals refer to it as "Locust Hill Cemetery in Chester, West Virginia"; however, geographically it is far far from the town itself in the countryside of Hancock County in Grant District. So, when I added it here (and to my own listings) I have it listed as "Locust Hill Cemetery, Grant District, Hancock County, West Virginia".
It is my opinion that placing it in the limits of a town in which it isn't can lead to more confusion generations to come, especially if it services more communities in a county because of its location in the rural area. I personally have had problems in my own family research finding cemeteries because they were listed in locations in which they didn't physically exist.
Also look at it this way. Sometimes, those rural cemeteries were founded way before the town they are listed in was ever thought of or founded; used by the farmer of that township/district mainly until population centers popped up in the neighboring areas of the county who then continued to use it for their needs. Another reason to keep it listed in Township/District if not in current town limits.
I hope this helps.