Seat height should be set for proper leg extension regardless of the bike. If it feels funny, could it be that the seat is more forward or further back? That or maybe it just feels funny because the bars are higher and/or closer/further from the saddle.
If I had to guess I'd say you are just feeling like the seat higher because your torso is in a different position due to different reach and bar height. Maybe those were different on your old touring bike as well.
Oh and one other thing... If you are measuring from the pedal axle perhaps the pedals themselves are higher. A quarter inch makes a noticeable difference. Heck, after a month on the road I get so settled in on the setup that 1/8 is noticeable, At that point I feel like the saddle is noticeably lower if I get on the bike with unpadded shorts (even when the pad is a thin one so the difference is pretty slight.
I like my bikes all set up as close to alike as possible wrt riding position. I like the same seat height, bar height and reach on the touring bike and the road bike. That means that I have my bars far lower than most tourists, but I find my road bike exceedingly comfy, so why wouldn't I just match the setup for touring too. I am in the minority on this though, so it may not be for you, still something to consider though.
The way I arrive at my starting setup for a bike is to set it up step by step as close as possible to my comfy road bike measuring the road bike and the new bike each step of the way. I start with the seat and then the bars. I allow for possibly tweaking settings after riding especially if the geometry is really different, but it is generally pretty much unnecessary.