I am always amazed what you accomplish with minimal gear, so I suspect that a focus rail and specialized software for stacking are not likely what you have in mind. An image like "Single Bloom" or "Tulip Light" seems to cry out for focus stacking so that the central subject has more detail.

On the other hand, for "The Colors" the leading lines from the petals and the gradation of focus produces an arc of subject in focus. This makes an appealing and unusual composition, so that "The Colors" is my favorite from the set.

In other words, my suggestion is to seek out compositions that are matched to the technique, as you did for "The Colors" and not stress about the shots that need a different technique.