The birdhouse of the soul in medieval art can have a few meanings--Google reverse image search shows that the two examples you picked illustrate two of the main ones, which is pretty awesome.

Survey says your first painting is a fresco from a Serbian Orthodox monastery that depicts the apostle Peter. He's carrying a church building on his shoulders to symbolize "on this rock I will build my Church," most likely. (From the same fresco series, Paul is not carrying the Church.)

Your second example is a depiction of patronage. From the Cappela degla Scrovegni, it depicts Scrovegni "giving" his church building to God (that is, paying for it).

So I guess in general, I would say that the little buildings represent either the Church or a specific church and express a relationship between the person involved and the C/church.

Medieval patrons and donors were frequently portrayed with miniature images that represent the object or building created under their auspices. Particularly when this served a Christian purpose, such as a church, a cross, or a prayer book, an image of the person whose donation made the work possible--when shown holding that miniature--was understood as a reminder to pray for her or him because of this good work. Thus the patrons were honored by being represented in perpetuity with the works they fomented while also reaping the benefits of prayers every time someone observed the donor portrait and called the creators to mind in prayer. Your example of the painted donor holding a miniature church is not, in fact, limited to frescoes but can be see in exterior sculpture on many Gothic cathedrals, on interior capitals of Romanesque basilicas, and in elaborately carved altar scenes. The same concept extends to liturgical objects such as illuminated manuscripts and bejeweled crucifixes for much of the Middle Ages.

The self-referential nature of this imagery plays out in a similar way through the inscriptions on works that credit donors with the act of making. The verb employed most often to refer to the individuals responsible for artistic creation, as it appears in medieval inscriptions from paintings to embroideries to architecture, is “made” (fecit). This word denotes at times the individual whose hands produced the work, but it can equally refer to the person whose donation made the undertaking possible. Thus a cross or a manuscript or a sculpted capital or an embroidered battle flag can bear an inscription that says Elisava or Gofridus or Ioannes and Maria "made me" (me fecit), eliding the differences we now perceive between patron and artist. Whereas today’s eye wants to separate these two roles in the creation of a work of art or architecture, the medieval view recognized that both were makers.

For recent scholarship on this topic, see 'Me fecit.' Making Medieval Art (History), a special issue of Journal of Medieval History, http://www.tandfonline.com/toc/rmed20/42/1