The generate alignment links within tolerance option is an efficient way to automatically generate parcel alignment links; however, it would be beneficial to have an optional checkbox that would allow you to specify to generate links only within the map extent. This option would allow you to have more control over where links are automatically generated.
Say there is an area you are aligning where the links to create are quite obvious, but there is another area where you would be better off manually creating links. This option would allow that to be a smooth process.