I'm not sure exactly where you think that there is a problem here. I don't see one.
In stock form, the front of your car has 7.2" of total travel. This is with the bumpstop removed. It is limited in both directions by physical limitations of the strut. From ride height, it is divided up roughly into 3.6" of droop travel and 3.6" of bump travel.
If the car is then lowered 1", by changing the springs for instance, the suspension will have 2.6" of bump travel and 4.6" of droop travel. At full droop travel, the spring will probably be loaded against the FCA with force. More on this later.
When you install a coilover kit on the strut, some things are now different.
If not properly chosen, the spring could artificially limit the bump travel by coilobinding before the strut bottoms out. In your case, this will not happen because the spring was correctly chosen.
If a much higher stiffness spring is used, then it is possible that the spring will come loose between the upper and lower perches, when the suspension is at full mechanical droop. This is a function of the spring rate, unsprung corner weight on that corner of the car, motion ratio and available droop travel in the strut at the ride height that you will be using. To understand this relationship, read through my post linked below.
I'm assuming that you've read the post. If you haven't nothing below will make any sense.
The tender spring that you purchased has a spring rate of 12lbs/in and is 4" long. This means that when 48lbs of force is applied to it, it will become coilbound solid. If you lower the car down onto the ground just slightly, there will be 48lbs of force on the spring and it will be coilbound. At the same time, there is 48lbs of force on the main spring which has a rate of 325lbs/in. This spring is only going to compress 0.15". This will barely be noticeable.
If you jack up the car so that there is only 24lbs on the springs, now the tender spring will be 2" long and the main spring will only be compressed 0.075" of an inch.
From your photos, it appears that this is what the suspension is doing currently.
Does all of this make sense?
In your e-mail to me, you mentioned that the front suspension will only have 2.75" of travel because of the bumpstop. I assume that you mean that the suspension has 2.75" of BUMP travel (from ride height to full compression). Is this correct? If this is the case, this is completely normal for the front suspension on your car.