EPA recognizes that there are situations where you will not know up front exactly how many acres will be disturbed, or whether some activities will even occur. If you are not sure exactly how many acres will be disturbed, you should make the best estimate possible and might wish to overestimate to ensure you do not run into the situation where you should have a permit, but do not have one. For example, if you originally estimated less than 5 acres would actually be disturbed and took advantage of the "R" Factor waiver, but you actually disturbed 5.5 acres, you would lose your waiver and may have to go through the permit process mid-stream. This could result in delays in obtaining permit authorization and costs associated with contract changes to implement permit requirements - in addition to being liable for any unpermitted discharges.
If you have a long-range master plan of development where some portions of the master plan are a conceptual rather than a specific plan of future development and the future construction activities would, if they occur at all, happen over an extended time period, you might consider the "conceptual" phases of development to be separate common plans provided the periods of construction for the physically interconnected phases will not overlap. For example, a university or an airport may have a long-range development concept for their property, with future development based largely on future needs and availability of funding. A school district could buy more land than needed for a high school with an indefinite plan to add more classrooms and a sports facility someday.