Boot between shaft log and packing

[JawsB40]

I am trying to install an Aqua Drive on my B40. The distance between the shaft seal and transmission is limited. Is there a reason that the rubber boot is so long adding a couple inches to the seal position? Ultimately I am considering having a new shaft log machined with threads and a packing nut inboard to give me the clearance I need. I am trying to leave enough room to renew the packing as necessary. Or I could incorporate a Tides Seal if water circulation is the issue. I have to be inventive here because my new Yanmar is difficult to align due the the hull design.