Best way in my opinion is a real example. There's too many technicals to go in to for each individual type of purpose/method; games, archviz, etc. So when I started I went through all the model packs I purchased and the ones I thought were the most useful in terms of production I emulate how they do it.
To answer your questions anything baked/merged is always difficult to edit as the buyer. If its a unique item with a particular look then its mostly ok - usually organic or hand crafted/painted things are usually not really in need of much editing if they look great or real-time assets.
If you plan on selling to archviz customers then real-world tileable full high resolution textures with materials separated as objects/object IDs are better. This way buyer can quickly darken all the glass at once, change the metal from gold to powder-coat black, etc. Real-world is the key here, if you set up your textures/uvs so they have uniform texel density then the customer doesnt have to resize things on their end they can just easily swap out your materials for theirs and it should work.
