Dan, it sounds like you are taking a responsible and careful approach to this.
If some of your aircraft don't have autofeather, you would be best to train for 'worst case' scenario, in that when the fertilizer hits the fan there may not be time to analyse whether or not the prop has feathered and whether or not to initiate a manual drill. It is usually best to do nothing than to do the wrong thing.
With that in mind, I suggest that you regard V1 as only a V1 for accelerate-stop being guaranteed. Unless your V1 coincides with an unusually high Vr, it is probably not a 'true' V1, in that following a failure at exactly that speed, continued acceleration under control to Vr then further to "V2" is probably not achievable with a prop windmilling and may not even be achievable with it auto-feathered (unless in very skilled hands). By definition, V1 can never be greater than Vr but could be equal to it or considerably less. But the very use of the term V1 implies that having suffered a critical engine failure, continued flight under control in the hands of an 'average' pilot is assured, and this is where if you are not careful, your pilots could be deluded. I am no Twin Otter guru, but from the little I know, when operating from limiting runways, rotation to take-off occurs at some fairly low speeds, i.e. below Take off Safety Speed.
As with many light twins, you should treat the time between "V1" and Take-off Safety Speed as a time when, if an engine fails, you must land as best you can. Better to hit something (hopefully not a brick wall!) at 50 knots wings level than to auger in from 50 feet with no control. On any given flight your exposure to this risk (i.e. unable to continue, unable to stop on the runway) is probably only in the order of 10 seconds or so. Quite an acceptable risk, given the very remote likelihood that the engine will choose those 10 seconds to cark it.
When doing your 'armchair' reviews of procedures, I recommend teaching pilots to leave any attempt to manually feather until above 50 feet and at or above TOSS. If you fly two pilots, PF flies, PNF identifies, PF confirms and PNF feathers......slowly......
The recent chilling video of the ATR 72 in Asia that went in at nearly 90 degrees bank angle should be compulsory viewing.
Anyway, keep up the good work!