I guess it is to be expected that a museum cannot be nominated for its artefacts (which are tangible),
The issue which would seem to prevent museum contents being inscribed isn't that they are "tangible" but that they are "movable".
I guess it would be said that
a. The Fresco items in the museum are described as "detached" and were not intended to be "movable". That argument could less easily of course be applied to e.g Giotto's Crucifix
b. All of the items complement/complete the main aspects of the proposed nomination and are not simply a collection of artefacts in a museum separated from their original context. Although they are not in their original locations are they not an "essential" part of the "close by" nominated "set" such that, without them, the full "OUV" isn't represented?
I note also that the museum contains items in its collection which are in no way linked to the 14th Century (Roman, Pre-Roman and paintings through to the 18th C). So - would any nomination exclude these? I guess not - many a city/town has been inscribed for OUV relating to a particular historical period but buildings not from that period are not "excluded" from the inscribed area.
I raised a similar issue in my review of Zeugma ( http://www.worldheritagesite.org/sites/twhs.php?id=5726
). In this case - whether the actual site could/should be accompanied in any nomination by the magnificent mosaics now housed for preservation and safety in the Gaziantep Mosaic Museum (in this case the museum isn't mentioned in the site's T List description - but it has only been constructed and filled recently). The entire collection on show there is from Zeugma and none of them were ever intended to be "movable" - although that act has surely been justified. They are undoubtedly a part of any OUV which Zeugma might have. If they had been moved to a museum "on site" at Zeugma rather than to a museum 55kms away would that have made any difference to the acceptability of their inclusion in a nomination? If they had been moved on site but relocated in a similar location to the original (i.e further up the hill away from the man made lake which had inundated them) would that have been more acceptable? I think of Abu Simbel and Philae which have been inscribed despite having been "moved".
A fair number of archaeological sites possess on-site musea which contain highly valuable and significant artefacts from those sites but I know of no example where these musea and/or their contents have been cited as part of the OUV. An upcoming nomination where this could be significant is Aphrodisias where the frieze from the Sebasteion is wonderfully presented in a purpose built structure and cast replicas have been placed on the original building where it still stands. Is that original Frieze a part of the site's OUV or not?? If so would it still be so if the museum had been built 5, 10, 50, 1000 kms away?
The only example I know of from "WHS History" where a nomination was rejected for being "movable" was that of the SS Great Britain iron hulled steamship in 1988. This is located in a dry dock in its home port and site of construction in Bristol.
Conversely there are a number of examples of where the contents of an inscribed site would appear to be "essential" for its inscription even if they are "movable". E.g would either of Stoclet or Plantin Moretus still have adequate OUV if the contents had been removed (this is actually an issue with Stoclet, is it not, since ownership varies as between contents and building)? Where the contents are a genuine part of the "original" their importance would be greater but quite a lot of what is on show in the Plantin Moretus house isn't originally from that house - e.g collections of maps etc. How much of it could be "removed" for the site still to be worthy of inscription?