Yes, I understand what you mean. I am convinced a custom would be my ticket. However, if this was not possible (say my requests were possible, but not do-able from Alembic (for what ever reason)), then I would consider upgrading.
Sure, it would be cheaper to upgrade your current bass/guitar, but like you said, there are many other factors that a newer custom would answer. I personally don't to upgrade my bass, I want to upgrade the whole body. The more I think about it, the more I want to do it. But whatever outcome, I will humbly accept what I have and be thankful.