If you use the Ceres storage engine for Graphite instead of using Whisper, you will avoid the problems of pre-allocation of space. https://github.com/graphite-project/ceres
I don't believe you can, during downsampling, merge multiple metrics with a specified aggregation. However, you can do this at the point of ingestion via aggregation-rules.conf. Documentation can be found here: http://graphite.readthedocs.org/en/latest/config-carbon.html#aggregation-rules-conf