It sounds like you're conflating meditation-the-exercise with spiritual and religious approaches.
Fundamentally they are unrelated. Taking it to the extreme one can consider the mind to be a process produced by the brain+, no soul involved. Taken that way, meditation is no different than weight lifting. The same way a muscle+ specialises itself depending on training (endurance vs strength vs explosive vs volume) the brain (and thus the mind) also specialises in whatever it gets most exposed to. The same way one can lay out a physical workout plan for a specific desired outcome (including rest), one can lay out a mental workout plan for a specific desired outcome (including rest). The latter is meditation.
Meditation may exist in religious contexts, e.g Buddhist or Zen, but even then many forms are in practice detached from any religious belief, with no koan or mantra. e.g Ānāpānasati (sit, and simply watch the breath) and Sōtō shikantaza (meditation with no objects, anchors, or content, striving to be aware of the stream of thoughts, allowing them to arise and pass away without interference). These are fantastic tools to unlearn bad (sometimes traumatic) mental habits, just like one learns to have smooth but effective muscle action instead of being tense and twitchy and forcing it through.
+ I'm using "brain" as a shortcut for a system that is vastly more complex, just as I use "muscle" for a system that is equally as complex.
