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A dyno run isn't any more stressful than doing that run to redline on the street, as long as the operator is careful.
As for relearning, since it's an '03, relearning is possible. If you've got a piggyback unit that can run the injectors independently with direct input from the MAF, relearning won't hurt you... but otherwise, you have to take it into consideration.
If you've got something like the Split-second AFC or the Unichip, it's an issue. The Unichip has a feature to spoof the O2 sensor to prevent LTFT from drifting, and one to switch maps (if I recall right, my Q had four separate maps) when a trigger was reached (temperature, AFRs, etcetera) or when you flipped a switch.
One guy on our Mazda board with a Split-second got around LTFT drift using an intercept for the O2 sensor.
And yes, tuning it yourself is risky unless you know what you're doing. And dyno time ain't free.
Like I opined earlier... not worth getting for economy... but if you're getting it for the extra power, consider whatever marginal gains you get for economy (and considering an 03 will be OBDII, which already runs stoich at low loads and cruising, they will be!) as a bonus.
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