There are a lot of tradeoffs in designing a woofer system and some of them may be in play in the differences you hear between the Merlin and the ATC.
For example, the Merlin is 89 dB efficient and the ATC is 85 dB efficient. The higher efficiency of the Merlin comes mainly from its woofer having a more powerful magnet. This more powerful magnet actually tends to reduce the level of the bass (and even lower midrange) region relative to the rest of the spectrum. If the Merlin’s woofer is then placed in a cabinet that is tuned fairly low, there will likely be a "sag" in the response curve above that, and this "sag" can extend up 3 octaves or more above the port tuning frequency.
If this is indeed what’s going on (or at least part of it), imo it’s the sort of thing that EQ can help with.
Duke