I think it's been high profile due to number of airprox's in London airspace, the most significant I can think of recent AAIB 9/2010 EW/C2009/07/07; There's many comments regarding the SID and cleared altitudes. In summary the aircraft misheard his altitude clearance and climbed to 4000' instead of 3000'. The controller in your instance clearly had concern maybe a similar thing had happened, you say when you explained you were in VNAV that was enough to re-assure him/ her you knew what you were doing following the SID. From the AAIB report
‘Controllers must remain alert to the potential
for incorrect or unexpected interpretation of ATC
instructions by non-UK aircraft operators and
take appropriate action to ensure any required
separation.’
Personally, I can't see an issue in you being cleared for the SID with the associated altitudes included in that clearence, selecting the highest level associated with the VNAV proceedure which you have to do to follow the profile.
Flying in VS or FLC with ALT cap is higher workload and could result in delayed climbing in the step giving higher rates of climb and distractions which VNAV avoids.
I'm not sure but if you selected the altitidues as you passed them with your VNAV would your AP/FMC recapture or amend the VPATH?
It would be interesting to hear what a controller has to say, maybe post in thier section 'ATC issues' too?