This question is really about European mortuary and funerary practices among the elite during the early modern period, as well as deeper sociocultural meanings that might have went with the experience of death and burial in a public space. How did people in early modern Europe understand burials in a public place? Of course, practices around death and burial are super important for understanding OTHER peoples' cultures, but I haven't given the meaning behind Western Judeo-Christian funerary and burial practices in the early modern period much thought. I thought of this question while standing in the cathedral in Sevilla and realizing that I was walking on top of the graves of many famous people. Today, it is easy enough for tourists to breeze right by these graves without giving them much of a thought, but this would not have been the case shortly after a person was entombed there. I find it interesting that funerary practices in early modern cathedrals essentially created ritual, performative, and spacial dimensions to death that intersect with natural biological processes in ways that I know absolutely nothing about.
How were bodies prepared for burial in such public places (both physically and ritually)? Did bodies undergo a process of embalming? Would any practices have guarded against the smell of decomposition or even possible public health dangers? Would flowers, incense, and perfume really have covered up the smell? Was decomposition just a normal, unremarkable part of the funerary experience or perhaps the smell of death had unique religious or spiritual meaning in the early modern period, which we no longer maintain in the modern world? In essence, how did people understand and perform death and decomposition in a public space?
Burying people inside churches began in already in the Middle Ages. Here in Scandinavia it goes back as far as Christianity itself; the first churches were private chapels built by wealthy families that'd likely encountered the religion abroad., and had themselves buried in these chapels. (the 10th century Kata Farm for instance) So nor was it, from the start, limited to cathedrals. It was considered a privilege to be buried inside the church, and thus a source of revenue as wealthy people made donations to be allowed to be buried there. (In these countries nobles often had patronage rights over 'their' church too)
So people were buried under ordinary church floors too, including wooden ones which accounts describe as smelling much more as the wind passed through them. I spoke just last summer with the very history-interested sexton at the church in Mariefred (built 1624, image, with all-wooden floors) who described having to go nearly from one end of the church to the other in the crawlspace under the floor (for some maintenance reason I can't remember) and explained how he had to crawl across bones and was bumping into skulls the whole way; it was so packed with them down there.
Anyway, most of your questions has the answer 'no'. They couldn't avoid the smell. There are many records of a nauseating stench of dead bodies in church in the early modern period. King Johan III complained in 1588 that there was such a stench of dead bodies in the churches, it made one "vomit and choke". (spy och storkna) A record from 1631 records a 6 year-old boy vomiting in the cathedral of Västerås due to a 'horrid corpse stench'. (en slem likstank) The chapter of Storkyrkan (the main church of Stockholm; now a cathedral but not at the time) had to adjourn a meeting in 1686 because the "stench and corpse smell" was too disturbing, and neither incense nor fresh fir twigs had helped.
As implied, the churches would try to mask the smells, and individuals would have pomanders, sachets and similar things to mask the smell. The stench and increasing concerns about hygiene is why the practice ended in this country in the late-18th and early 19th century. Georg Carl Brunius, an antiquarian and responsible for the renovations at the time of Lund cathedral, wrote in 1836 how, despite it being many years (about 20) since the last burial inside the church, the stench arising from the crypts was more than enough to suffocate any desire in him to open them for research, had he had permission to do so.
Regarding "Judeo-Christian funerary and burial practices" there's really no such thing; the traditions are quite distinct. Dead bodies are ritually impure in Judaism; as are people/things which come in contact with them and spaces where they are kept. Traditionally, bodies are not brought inside synagogues for that reason; so burying someone inside one would be less than ideal to say the least. (I'll leave it to any historians of Judaism to say whether it ever happened despite that, I don't really know. But it's certainly not the usual thing)
Source for the quotes other than Brunius:
Göran Malmstedt - Bondetro och kyrkoro: Religiös mentalitet i stormaktstidens Sverige, pp47-50
