It depends.
If the unit is full out at acceptable return water temperatures I like the certainty of sealed combustion, direct vent combustion, as conditioned air is not be ejected nor free outside air introduce to the living space. The ModCon will normally operate in the 88% combustion range while working at the hottest design temperature around 180°F. This is better than the best atmospheric boiler and the difference in stack temperature is beyond debate 450° vs. 150°F conservatively.
However, if the unit does modulate and shutdown in cycles below 5 minutes, combustion efficiency will suffer as DANA suggests. Electrically draw increases as well and the cycle life of the various system components will be shortened.
The worst mistake one can make when specifying a condensing boiler is to assume modulation gives you a pass on doing a proper heat load. As is born out by Dana's graph the real savings are in those low output, low temperature modes.
A boiler too big for the space, is more bitter than death.
A condensing boiler is properly sized for maximum output and minimum output according the the block heat load of the structure it will serve and the minimum output for the zone that is both the coldest (highest heat load per square foot) and the smallest relative to other rooms. For instance, on a recent remodel an expensive sun room was installed some ten years ago and the owner-in Woodbury, MN-found the new "sun" room quite cold in all but sunny weather. In fact, for three months out of the year no one could be in the 62°F room.
Since the system was forced air and three registers, improved sliding glass doors and extra insulation in the crawl space and sub-floor had no effect drastic measures had to be taken. The problem of course was that the sun room presented the largest load per square foot, needing more heat that the rest of the house in all weather conditions, save sunny mild days-not common in Minnesota. The answer was to radiate the floor beneath and using the existing water heater as heat source. The water heater serves this micro-zone best by virtue of its relatively high mass allowing 3800btuh to be delivered to the space without short-cycling even the first 75 m stage of the 150 mbtuh furnace.
In the perfect hydronic design a modulating, condensing boiler with properly tuned out door reset would never shut down on any limit and easily reach its 98% potential combustion efficiency with no penalty on the system side, save circulator operations and pipe loss.