Squawk,
Accelerating at 1000' or 3000' is not significant as far as aircraft handling goes (disregarding airport specific obstacle requirements). In the situation you described I would PULL selected speed, and then PULL open Climb. Once you reach 3000' select 250 kt, accelerate and clean up. If necessary due to busy airspace PULL selected speed, PULL VS and adjust vertical speed. On reaching 3000' select 250 kt, accelerate and clean up.
Now, why is you new operator using 3000'? Because it is in PANS OPS DOC 8168. There are two noise abatement procedures described here. NAPD 1 and NAPD 2 and you can find them described in "Appendix to Chapter 3" in Doc 8168, Volume 1. They both, with some difference in wording, call for "At 900 m (3 000 ft) above aerodrome elevation, accelerate to en-route climb speed." This is why your new ops procedures call for the 3000' acceleration. The procedure as such, in PANS OPS, is not new. However, I believe that last year the rules changed somewhat and if I am correct you are now to follow this procedure on every departure unless local procedures call for a different climb/acceleration schedule. I have not been able to find a reference to this but maybe some else can provide this?
If you keep this in mind before every departure then you can change the acceleration altitude on the PERF page before takeoff and you will not have the "problem" you described above. When given clearance to higher alt/lvl just delete the constraint.
Good luck!
CP