<p>Other than the most obvious issue with the filament kinking in the tube, what other issues could arise when trying to print flexibles (<em>i.e. TPU/TPE, Nylon, etc.</em>) with a Bowden style extruder setup? </p>

<p>Can the kinking issue be alleviated by a well-constrained filament path (<em>proper ID</em>) in a properly sized Bowden tube?</p>

As a user of an UM3E, which uses Bowden tubes and has TPU as an available material, I can tell you that the kinking issues can be alleviated or downright avoided.
I've printed quite a few things with the Ultimaker-brand TPU 95, and never had problems with kinking in the tube.
Ultimaker uses 2.85 mm filament, with Bowden tubes adapted for those and a rear motor, i.e. the motor is on the back on the printer and not right on top of the print head.
I personally wouldn't consider Nylon as one of the really flexible material, but that's my opinion. Never had kinking in the Bowden tube with Nylon either in my UM3E.