Pretty sure we've had this question before but anyway, I wouldn't dismiss items as being luxury just because they are from large leather goods companies. Hermes is as big as any other international fashion houses now, and lots of brands, even those that started as fashion houses have bags for connoisseurs, if you know what to look for in terms of quality you will find it.
Perrin of Paris - once a glove maker, now do amazing bags too
Moynat, Delvaux and Valextra
Tanner Krolle (owned by the owners of Chanel) mostly made on application
Asprey, mostly limited of a kind pieces in precious skins
Launer, handcrafted, bespoke considered
Gucci have some amazing bags. They do 'made to order' on certain styles of bags (BTM, Stirrup, New Jackie) their women's loafers. They also do made to measure shoes and tailoring for men (but they'll make for women too if asked)
Pickett of London do bespoke and for a comparatively reasonable, their bags are handcrafted and finished, and all but a few have suede interiors
Vintage mid-century bags of long forgotten names like Bellstone and Korret, unbeatable value with often quality that can only be dreamed about
Ettinger London, handcrafted but plain limited styles
William and Son, off shoot of Aspreys,very limited quantity of handcrafted bags
Patey and similar for bespoke hats
Savile Row London is still choc a bloc with bespoke gentleman's outfitters and tailors
Amazing little one off botegas in Italy, especially around Florence, many do MTO and personalisation. There is a special market where artisans (including those that work for large companies) sell bags, and will make you bespoke versions. Just because something doesn't sell on the Net doesn't mean it doesn't exist