'and the chauncels shall remain ...
as they have done in tymes past', so states the rubric before Morning Prayer in the 1559 Book of Common Prayer. At Snarford in Lincolnshire, Sir Thomas St Pol, seems to have made a very specific statement as to how he wanted the chancel of his parish church to 'remain' and it was a radical break from the medieval past. When he died in 1582, his canopied monument was erected right at the east of the chancel as close as practicable to the east wall. Thus leaving no room for the reconstruction of a stone altar or even the positioning of the holy table 'altarwise' at the east end of the chancel. The holy table must have stood west of his monument in the body of the church and presumably lengthways, the space is now occupied with a twentieth century 'English' altar. On the monument itself Sir Thomas and his wife Faith are portrayed as very much people of the Reformation, clasping their prayer books to their chests.
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http://www.ecclsoc.org/postreformationtables.html
In spite of the temptation, I will refrain from commenting on the current state of the Church of Rome.
What made the c19 ritualists think that churches were intact at the date of 1548-9 was the survival of inventories of medieval furniture. But they were inventories of objects removed from churches, not what was still in use. The scholarship of J. T. Micklewthwaite, for instance, laid the foundation for meticulous and beautiful late-medieval reconstruction.
Comper himself often researched surviving inventories before restoring medieval churches. But from Dr Lee and the mid-Victorian Directorium Anglicanum onwards the appeal to the Ornaments Rubric for externals was based on a misunderstanding of the historical evidence. In another, quite different sense, Praise God that it was because it led to the building of the finest churches of the late Gothic Revival.