First off, I misremembered the amount of insertion loss - about 3dB is the high end, but that's still significant since that means you'd need twice the amplification to get the same SPL. Generally it's more like 1-2dB.
Think about it this way: baffle step correction, if present, is dumping signal to ground. Any notch filters if present are dumping signal to ground. Padding the tweeter down to match the woofer either involves series resistors (turns power into heat) or a voltage divider that dumps signal to ground. All of these things are done at small signal levels (line level, generally) with op amp filters in an active speaker, or in DSP. There is no insertion loss for those filters as they're buffered, or in the case of DSP, aren't even in the analog realm. Instead of using a voltage divider to dump amplifier signal to ground, you just send the amplifier less signal, or do any required compensation at small signal levels.