I'm not ferram, but the reason the FAR to stock, universal preset penalises flying in a vacuum is to try and spread the load of 'paying off' the extra delta-v you gain from being able to fly a more efficient ascent across both your atmospheric flight and your vacuum flight. The reason the adjusted preset has such a heavy penalty for flying in atmosphere is that it has to front-load this same ~1000dV penalty to the first 35,000m of altitude, before the atmosphere becomes so thin as to not affect your Isp anymore. Generally speaking it shouldn't significantly affect your rocket design compared to the universal preset (since the idea is to make you carry more fuel into orbit, meaning you need more fuel and possibly thrust in your lifter), but your ascent may need to be more vertical to get enough efficiency out of those engines to reach orbital speed before you run out of fuel.