Tradition was to marry in the bride’s church, so I’d favour Lucinda being Methodist (her husband might also have been too of course). If she were still Church of Ireland, I’d have expected her to marry there.
There are 2 Methodist Meeting Houses in Seagoe. Both were Wesleyan. (I see from the 1911 census that the Lutton family were Wesleyan). Ballinacro has baptism records from 1845 onwards, Bluestone from 1839. (Copies of both sets in PRONI). Prior to those years the congregations would have used the Church of Ireland for their baptisms.
If you are unable to go to PRONI yourself, you could employ a researcher. Researchers in the PRONI area: http://sgni.net
The property in Breagh that Jonathan had is quite interesting. Anomalous really. It was quite a big farmhouse, with plenty of outbuildings, but on a tiny piece of land (just over 3 acres). Most farmers would struggle to feed a family off 3 acres. That was subsistence farming. (The property today is on the Gilford Rd. Tyremaster have premises on the land, judging by the modern map). Jonathan’s death certificate describes him as a farmer, rather than “Gentleman.” The value of his estate when he died was £50 5 shillings. So not penniless, but not a really wealthy man either. If you go to the 1901 census and search the house & building return, you will find that the farm had solid walls and a slate or tile roof (as opposed to mud walls and thatch for example). There were between 7 and 9 rooms, and there were 8 windows at the front. There were 14 outbuildings. The enumerator assessed it as a 1st class building. The page with the details of the outbuildings is missing but it’s there in the 1911 census. There was a stable, a coach house, cow house, calf house, dairy, piggery, fowl house, boiling house, 2 barns, turf house (ie a shed for storing peat for burning on the fires), potato house, workshop, shed and a store. The farmhouse looks to have been one of the biggest in the townland.
My interpretation of the will is that all these buildings are the lands etc that are referred to in the will. If he had lands in other townlands it would have been normal to specific them.
Answering your query about Thomas Whalley, I made a mistake with the year of his death. He too died in 1884, just outliving his brother by a couple of months:
https://civilrecords.irishgenealogy.ie/churchrecords/images/deaths_returns/deaths_1884/06329/4815097.pdf