No need to worry as far as MTB access goes, at least at this stage, though two tracks are to be closed off to MTBs. They are the two eastern tracks in Bunjil that connect Rodger Rd to Long Gully Rd. One of these is no fun to ride anyway - loose, eroded, ugly, fenced on both sides of the trail. It's a pity that the other one - Mineshaft Tk - is to be designated walkers-only but it's hard to argue against it when the trail goes directly down a loosish steep fall line at an angle greater than that recommended by IMBA.
Edit: The management plan concerns only the Panton Hill Bushland Reserve System managed by Nillumbik Council. It doesn't affect National Parks (e.g. Kinglake), Parks Vic land (e.g. Boomers Reserve), Melbourne Water land (e.g. Sugarloaf Tk) or other council land (e.g. verge trails).