No don't disregard it - just realize that it's one of many factors in the penetration half of the terminal performance equation (expansion being the other half)....along with speed (AT the point of impact), bullet construction and how that relates specifically to the speed at the point of impact, and sheer weight without regard to sectional density. Sectional density can often be THE most important factor in penetration. But sometimes it's not - when it's trumped by weak construction and high velocities or just sheer weight (momentum), which counts for a lot. Here, since the weights are the same (100/100), the SD does count for something - a lot even, but it's still a minute marginal increase in SD between those two bullets. Really, it's all about bullet construction in the end, and MATCHING that construction to your speed at the point of impact (or range of possible hunting point of impact distance scenarios), and the game in question (size, anatomy, etc.). So for choosing a chambering, go with what you like or what your gut tells you.
Making the hit itself in the right place is far more important than anything else, so that bodes slightly in favor of the .25-'06 because the extra vel can help you minimize wind-drift-estimation error and drop-estimation error. In other words, making the hit in this close of a call trumps the terminal ballistics differences, and more vel is always better for making the hit, espec. on the windy pronghorn plain. So if you think you might have trouble crawling within 200 yards every time (where the .243 would be perfectly fine), then you might lean toward the .25-'06, just for a bit more velocity. The only downside is more recoil, more cost, longer action, and *possibly* a tiny bit shorter barrel life. Another advantage of .25-'06 is bullet stability / accuracy. A 100 grain lead/copper bullets is at the edge of what 1 in 10 .243 can stabilize, and a 1 in 12 .243 might NOT shoot it. But it's in the "middle" of weights for the standard .25-'06 twist rate, so all .25-'06s should be able to shoot any 100 grainer, including a gilding metal bullet.
I hate to recommend .25-'06 over my beloved .243 chambering, but for a dedicated pronghorn rig, it's tough to beat. Besides, you don't NEED much penetration to completely blow through a speed goat, even quartering. And in the event you think you do, you can always go premium bonded bullet. Heck, a guy on here was just showing his WY speed goats taken with a .22-250 and a bonded Nosler 64 gr flat point... bonded yes, but ALL .224 bullets have a pretty poor SD, including that one.
In the end, just keep in mind that making a good hit is by far the most important thing of all. Either one will do if you practice and know your rifle and load. But in high winds (i.e. SE Wyoming, etc.), the .25-'06 will shine a bit better, especially past 200 yards. Either chambering will easily do the job terminally, once you pick the right bullet for your rig and situation. In fact, if I was using .243 win on a speed goat, I'd use a gilding metal 85 myself - something like the Nosler E-Tip, or even a non-premium 85. But in a .25-06, I WOULD use a 100, because that's the sweet spot for MV/BC in that caliber. So the comparison *itself* is probably not a relevant one, unless you're going to also shove this rifle into the mulie role (remember, you may have both tags in your pocket- pronghorn and mulies - in that event, with a .243, I WOULD want a 100 gr bullet over an 85, most likely!)
You see what I'm saying? .... This is what I'd want:
1. Dedicated pronghorn rig, .243: Premium OR non-premium 80 or 85
2. Dedicated pronghorn rig, .25-'06: Non-premium 100
3. Dual-role, including mulies, .243: Non-premium 95-100, OR premium 85 [But NOT a non-premium 80 or 85]
4. Dual-role, including mulies, .25-'06: [Still] a non-premium 100...or a non-premium 115-117.
...if that makes sense. Just my .02. No reason to pay for premium bullets if there's no need to. But then again, there are exceptions to that. If I think the mulie encounter could happen under 100 yards, where a non-premium 100 grainer could explode, then I'd opt for a PREMIUM 100 or non-premium 115 in .25-'06. But I sort of discounted that possibility because the whole subject here is plains & desert, where the pronghorn roam (and some of the mulies do too - and some elk & cous deer for that matter)...point being that longer shots are the norm and a shot under 100 would be unlikely. So lemme ask you - is this solely a pronghorn rig, for sure?