Input clipping has nothing to do with extension. There are loads of threads about it in the communities on the MiniDSP website. Even discussions that include their staff.
I don't understand what you are saying, if you use too much Eq, then a driver can run out of excursion, you can clip the amp or both.
Here are two designs I have done. I have modelled the optimal box, and mine agrees with the Parts x-press model. I have also done a sealed alignment. The driver is too big to fit in the optimal box, so I made it large enough for the driver to fit. In any case this driver is totally unsuitable for sealed alignment.
I can not sugar coat this as this is not a good driver, and is not really a sub, as it can not reproduce the last octave. In addition the specs have embellished the truth in that this is NOT a 1200 watt driver at bass frequencies as you will see in the attached graphs.
I will only go over the vented alignment as the sealed alignment is not worthy of discussion as F3 is 70 Hz, and there is no room for any Eq, as the driver quickly runs out of cone excursion and the response shows that in that application the driver is a classic "thumper" driver beloved of car audio enthusiasts.
So lets return to the vented alignment. As I stated before, the free air resonance of a driver Fs absolutely sets the lower limit for a vented alignment. Attempts to Eq below that bottom the driver. The driver decouples from the box below that point and large stroke excursions of the cone take place with output falling at 24 db. per octave, resulting in fatal driver damage.
The first and second graph NA and CA confirm what I have just told you. AP shows you that available output is limited below 100 Hz or so. EP shows the power the driver can handle plotted against frequency.
CD the cone displacement graph shows that the driver is significantly power restricted below 80 Hz.
VV the vent air velocity shows that port is correctly configured with the vent air velocity below turbulence at 20 msec.
I shows the impedance curve and that optimal box tuning is 35 Hz.
The last two graphs show phase response and group delay.
From the description of the sound you describe in your first post, I can be certain that what you heard was driver bottoming. Your description is classic and the model shows that this speaker is highly susceptible to driver bottoming.
Now I understand that this data will be very disappointing to you, as you have put a lot of work into this, to say nothing of the expense. However all of us DIYers have had failures, including myself, especially in the early years. You have to regard these episodes as learning experiences. In fact I think failures teach you more then success.
Certainly I and others remain ready to assist you in your next project. Do not be disheartened.