I am in complete agreement with your post. Far too much lip service given to the importance of maintaining manual flying skills while having a culture of "I'm not sure that's appropriate right now" or "Best not incase it goes wrong". Airlines should be open to these minor deviations in the knowledge that they'll come back to benefit them on a stormy night some day in the future. A lot I think comes down to culture within an airline, while the manuals can all say one thing the practice can often differ in a more conservative way towards not wanting to be found out to be lacking in manual flight skills.
99.9% of times minor deviations, overshooting the loc, flying 6/7 knots fast for a couple of seconds etc will have zero effect on the safe outcome of the flight and I think we need to realise that and hold ourselves to appropriate standards, not that of a computer.
I agree cloud doesn't serve as a reasonable excuse not to handfly unless at minimums though I will throw in one further area I feel automation is appropriate, and that is close tight parallel approaches ala SFO etc, where using at least FDs to join the LOC is appropriate given the fact you'll roll out only meters off the side of another aircraft.
I'd also like to see as you said, OEMs include the equivalent of CDI's for RNAV approaches to enable them to be handflown raw data as well.
I also think it's important that we don't get drawn into an "The automation can do it better" debate. I'm fully aware that it can most of the time, there are few things I can do better than an autopilot, save for perhaps thrust control on a stormy night where certainly the Airbus' A/T lets itself down frequently, but for the most part I know I am at an absolute best, as good as the autopilot, and in most cases not so. The importance comes in being good enough, being able to fly within the tolerances, being able to correct deviations before they develop etc.
Just because one can not totally nail a VOR or ILS approach bang on the needles the whole way down does not make it any less safe; a 1/4 dot high or low, left or right quickly corrected is not an issue, and while the AP may not have done it, that doesn't mean we should abandon the maintenance of our handflying skills just because of that.