J.C. wrote:

Perhaps you missed my original post. I do use raised beds. The
purpose for the cups is to regulate the amount of water as per the
specifications in the book "Square Foot Gardening". My only question
is, is there any reason why I should NOT plant the entire cup when
moving from the greenhouse to the garden, instead of taking the plant
out of the cup and planting it?

It will definitely constrain the roots, and perhaps make them rot. If
you put the water at the base of the plant so it goes into the soil, the
roots will grow to be wherever they want to be to capture that water.
That may be where they would have been in the cup (or beneath it), or
not. Plants evolved to be smarter than you when it comes to where their
roots should be, and the ones you want to grow have evolved to grow in
soil, without cups.