So does a target curve need to be adjusted to try to deal with severe peaks and valleys in my room measurements?
The target curve is what you want your measured response to look like. The aim is to make your measured response look like the target curve. The process is:
1. Measure your speakers in room frequency response.
2. Calculate the EQ required to bring your measured frequency response closer to your prefered target curve.
3. Apply this EQ to the signal going into your speakers.
4. Re-measure the in room frequency response with EQ applied.
If this has worked, then your re-measured response will be closer to your target curve.
My understanding is that not all severe peaks and valleys can, or should, be EQ'd. This is where it starts to get more complicated and you have start to learn about room accoustics and the causes of the peaks and valleys - especially in the lower frequencies.