I've been considering the external antenna that has a refresh rate of 5 times a second. (I believe this is correct.) Tom will chime in and inform us all about it.
I do know what you mean though. If I mark a waypoint by scrolling the cursor to the center of a brush pile I like, It gets me close to it. But, I take into consideration that the internal GPS Antenna (My HDS-8 Head unit) is a good 3.5' away from my LSS-1 Transducer and about 3' away from my 2d Transducer.
When I mark a waypoint, it's marking the spot of my Head unit, not the spot my Downscan is showing.

With the external Antenna, I can mount that over the top of either transducer within inches of it. Not only would I have a faster refresh rate as to where I actually am, I would be marking the spot more directly. Also, when I am trying to zero in on a waypoint, I always have the GPS zoomed in as far as it will go. It will not show the waypoints if I'm aways from them, but I will follow the trail lines that are left in the memory until the waypoint shows.

If anyone knows where I can find a bargain on a new 4000 antenna, lemme know.