Yes you are much worse off ... I did an explanation in the weekly simple questions thread, which I'll just repost here:

...

OK. Let's say we want to go to Duna and just did our refueling in orbit around minmus. I'm going to use this online calculator for the transfer burns. . Scenario I: We do a direct burn from minmus. I will neglect the oberth effect around minmus. Don't know how to calculate that correctly. ;) But I suspect the difference in delta v is as miniscule as minmus gravity. So we basicly escape Minmus (70m/s) and then do the transferburn to duna from a 46400km orbit ... because that is Minmus' orbit around kerbin. The transfer burn will be 663m/s according to the online calculator. All in all: 733m/s . Scenario II: We escape Minmus, drop our periapse into low kerbin orbit and then do the transfer burn at periapse. I'm going to use the values from the more accurate delta v map now. Escaping minmus and dropping the periapse takes 70m/s + 90m/s. In LKO we would have to do a transfer burn of 1050m/s (online calculator). But since only our periapse is at LKO altitude, we have saved 930m/s because our apoapse is already out at Minmus' altitude. That means we only have to burn 120m/s at periapse. All in all: 280m/s . That makes a difference of 453m/s !!! By extension, this means that we can bring a smaller/lighter ship which will be easier to launch from Kerbins surface aswell. Conclusion: It is way more effective to drop your periapse down to Kerbin for your transferburn! . By the way: The delta v map and the online calculator aren't 100% consistent. But 450m/s difference is enough to overlook any errors that might have occured because of that.