I only use (an old copy of) Family Tree Maker as a viewer for GEDCOMs I download from my online trees at Ancestry, so I can't speak specifically to best practices for the new FTM. However, this is what I do in Family Historian.
To simply matters, I assume for now that I'm not using the Ancestral Sources add-on to aid in the data entry process.
- I create a multi-media object and attach the media to it.
- I create the source and associate the multimedia object to it.
- I turn on Family Historian's Auto-Source Citation feature.
- I fully extract all the data in it. By this I mean, I create people, facts, events, etc. and Family Historian automatically links these to the appropriate source.
Special case: if the item is a group photo, I use the feature in FamilyHistorian to frame each person's face and associate it with the proper individual.
Ideally I rarely add data first and then attach media later. Images which are categorized by Ancestry as "citation media" are associated with the source record they belong to. Photographs of people are associated with the people.
I could see where one might want to associate a photo with a fact, such as a photo of a house with a fact like a census or residence event. However, I don't want those photos synced with Ancestry, so if I were doing so in FTM, I would mark all those photos as private so (as I understand it) they wouldn't get uploaded as part of a sync.
You asked "And are there any side effects as a result of linking to source citation instead of fact?" but to me, the question should be the other way around.
I generally work on Ancestry's online tree system, and when I have access, I save items to people's profiles from fold3 and Newspapers.com. Those show up as Media items in the profiles of the people, so I don't know if those count as "Media linked to facts".
On her Ancestry Desktop Education series (the "Barefoot Genealogist" videos), Crista Cowan talks about best practices about photos on Ancestry. When time allows, I'll link to those videos here.
For more thoughts on this, see my answer to the related question How many sources/citations is too many?.