The only chapel ("capela") I can find in Porto de Mós appears to be at the Ermida de Santo António. So maybe this is the one ....

front (the "chapel"?)
http://k41.pbase.com/o3/21/4921/1/89688756.nKfm3teZ.Porto_Mos6131.jpg

back (the "apartment"?)
http://farm3.static.flickr.com/2013/2108934211_6c8af3d234.jpg?v=0

The town's churches are small also. The population is less than 2000 people even today.
200 victims may be an over-statement, as the actual eye-witness did not seem to note crowding.
The eye-witness did not note that the door to the "apartment" was either locked or showing burn damage. The description seems to imply a fire started inside the apartment, near its center. The floor of the apartment was so little damaged that it could still be traversed after the fire died down.

Carbon-monoxide poisoning, then post-mortem burn damage to the poor victims ? Grotesque and frightening expressions need not imply a violent death, but instead skin and tissue damage.

In any case, rather a baroque way to have arranged things, if there had been indeed some atrocity. Perhaps Esdaile and Oman (and so on) were (are) jumping to conclusions ?