I don't think you can make a backward-compatible 32-bit without changing your code. It's just one of those issue with backward compatibility.
One solution is to figure out what functions are missing, and then to make a function that replicates it. You could also use a switching function based on version. Some function may exist in the file exchange.
At some point, you'll have to decide if it's worth the time and effort to make and maintain a 32 bit version. Forcing users to use 64 bit isn't a bad idea considering 64 bit is better. Plus, if you have to compile 32 bit and 64 bit, each with different codes, then debugging and software development will become very complex.
function varargout = myFcn(varargin)
if verLessThan('matlab', '9.0.1') %9.0.1 is 2016a
[varargout{:}] = my_adaptation_of_matlab_fcn(varargin{:}); %you have to rewrite code
else
[varargout{:}] = matlab_fcn(varargin{:}); %matlab function in new version
end
