If you want to get the absolute best fit, performance and trouble spots, spend the extra bit of money and buy from a ski shop - ideally from the people who have been working on your boots if it is a good, competent shop. They will know your feet and issues. It may be a combination of punching out the shell where needed and properly sizing the liner for your feet and the boot, in light of your performance needs. Judging from your concerns, I think people who have done a lot of these liners are the best way to go.
The proper aftermarket liner with fill up all the empty space, but it may not take care of your pressure points without extra work, so you may be going back to the fitter anyway.
A good fitter will pad your problem areas to create more room for them, but the shell may also need to give in those areas to allow the expansion. At least, that has been my experience after putting in an Intuition Pro Wrap Liner into a newish pair of Salomon XMax 100's. I shell sized down, and I have a shell fit of about 10 mm. The custom shell was heat molded, expanding the 98 mm. last to my 105 mm. forefoot. The seller has worked on my various boots for about 7 years and knows my feet and "issues" well. I thought I wanted an Intuition Pro Tongue, but he told me that the Pro Wrap would fit over my instep because it had more volume above my instep. I still had some issues with my heel lifting, which he resolved by gluing on a broad foam shim over my instep on my left boot. At least for my foot, I don't think the Intuition liner had a well defined heel pocket. I still get a tiny bit of lift there, but not enough to affect performance. Would a Zip fit have been better? Don't know.
Depending on the Intuition Liner chosen, the liner may stiffen the boot somewhat.
Other than that little bit of slop in the heels, I am getting no movement anywhere now, and the boots are performing well. But that also includes canting, alignment, and various punches. I hope this is useful to you.