The antenna doesn't care what mode of operation you use.
Due to the larger diameter coil in the 5000, it IS a better antenna over the 1000. You would need instruments to measure the difference however. In other words, with all things being equal, I'd be suprised if you could hear the difference between the 1000 and the 5000, but it could happen.
If you use 1K+, get the 5000, if you run under 1K, get the 1000.
I run a 1000 with a pair of 2879s. Everyone hears me just fine!