This question refers to all variants of the Carbohydrate Builder, including those that interface to the Glycoprotein Builder.
For most monosaccharides, the aglycon will make very little difference to the molecular structure. Even for ketoses (see image below), the steric interactions primarily involve exocyclic rotations around highly rotatable bonds. So, in most cases the choice of aglycon should reflect the end goal of the build rather than concerns about structural implications. In most cases, OH is sufficient. The OMe and OtBu options were originally provided mostly for researchers desiring to run simulations of those glycosides for comparison with experiment. Of course, all systems are different. If in doubt, build the structure with different aglycons and see for yourself.
Here is an image of the interactive, point-and-click interface to the Carbohydrate Builder, showing the aglycon options: