Well this is a an implementation of what you say, done in prolog exactly to your specifications. Your "Merge" is actually a function called transpose (in the context of matrices), and this happens to be in one of the SWI-Prolog libraries!
1 ?- [user].
|: mergeandmap(Bss,Ls) :- transpose(Bss,BssT), write('Result: '), maptostrings(BssT,Ls), write('\n').
|: maptostrings([],_).
|: maptostrings([Bs|Bss],Ls) :- write(' '), zipstringbits(Bs,Ls), maptostrings(Bss,Ls).
|: zipstringbits([],_).
|: zipstringbits([0|Bs],[_|Ls]) :- zipstringbits(Bs,Ls).
|: zipstringbits([1|Bs],[L|Ls]) :- write(L), zipstringbits(Bs,Ls).
|: :- use_module(library(clpfd)).
% library(error) compiled into error 0.01 sec, 10,056 bytes
% library(apply) compiled into apply 0.02 sec, 16,256 bytes
% library(lists) compiled into lists 0.00 sec, 13,404 bytes
% library(pairs) compiled into pairs 0.01 sec, 4,772 bytes
% library(clpfd) compiled into clpfd 0.32 sec, 367,328 bytes
|:
% user://1 compiled 0.44 sec, 369,348 bytes
true.
2 ?- mergeandmap([[0,0,1],[1,0,1],[0,1,1]],[a,b,c]).
Result: b c abc
true .
3 ?- mergeandmap([[0,1,1],[1,0,1],[1,1,1]],[a,b,c]).
Result: bc ac abc
true .
4 ?- mergeandmap([[0,1],[1,0]],[a,b]).
Result: b a
true .
5 ?- mergeandmap([[0,1,1,1],[1,0,1,0],[1,1,1,0],[1,1,1,0]],[a,b,c,d]).
Result: bcd acd abcd a
true .
6 ?- mergeandmap([[0,1],[1,0],[1,0]],[a,b,c]).
Result: bc a
true .
7 ?- transpose([[A,B,C],[D,E,F],[G,H,I]],X).
X = [[A, D, G], [B, E, H], [C, F, I]].
Writing your own transpose function is a little more involved, as I decided to have a stab at it myself. After a while I did manage to get to a very neat solution, which by design, is able to accept lists of lists even when they're not rectangular! (Though it's still not as flexible as would be desired for use in mergeandmap unfortunately). Here's the code:
1 ?- [user].
|: transpose(Rs,Cs) :- emptylists(Rs),emptylists(Cs).
|: transpose([[X|R]|Rs],[[X|C]|Cs]) :- headsandtails(Rs,C,NRs), headsandtails(Cs,R,NCs), transpose(NRs,NCs).
|: headsandtails(Xss,[],[]) :- emptylists(Xss).
|: headsandtails([[X|Xs]|Xss],[X|Hs],[Xs|Ts]) :- headsandtails(Xss,Hs,Ts).
|: emptylists([]) :- !.
|: emptylists([[]|L]) :- emptylists(L).
|:
% user://1 compiled 0.07 sec, 1,208 bytes
true.
2 ?- transpose([[1,2,3,4],[5,6,7],[8,9],[10]],Result).
Result = [[1, 5, 8, 10], [2, 6, 9], [3, 7], [4]] ;
false.
3 ?- transpose([[1,2,3,4],[5,6,7],[8,9,10,11],[10]],Result).
false.
4 ?- transpose([[1,2,3,4,5,7,8,3],[5,6,7],[8,9,10,11],[10]],Result).
false.
5 ?- transpose([[1,2,3,4,5,7,8,3],[5,6,7],[8,9,99],[10]],Result).
Result = [[1, 5, 8, 10], [2, 6, 9], [3, 7, 99], [4], [5], [7], [8], [3]] ;
false.
Basically how this works, is it checks the top left elements of the transpose and original are the same, and checks that the top row of one matches the left column of the other, and vice versa, then checks everything else iteratively until there's nothing left to check.
The cut operator ! on the emptylists predicate stops the answers growing off to the right with more empty lists, and means that it can terminate on trying to transpose something which doesn't have one (where it just keeps adding them and always fails to find an answer).
In summary for an all in one solution this is all the code you need:
mergeandmap(Bss,Ls) :- transpose(Bss,BssT), write('Result: '), maptostrings(BssT,Ls), write('\n').
maptostrings([],_).
maptostrings([Bs|Bss],Ls) :- write(' '), zipstringbits(Bs,Ls), maptostrings(Bss,Ls).
zipstringbits([],_).
zipstringbits([0|Bs],[_|Ls]) :- zipstringbits(Bs,Ls).
zipstringbits([1|Bs],[L|Ls]) :- write(L), zipstringbits(Bs,Ls).
transpose(Rs,Cs) :- emptylists(Rs),emptylists(Cs).
transpose([[X|R]|Rs],[[X|C]|Cs]) :- headsandtails(Rs,C,NRs), headsandtails(Cs,R,NCs), transpose(NRs,NCs).
headsandtails(Xss,[],[]) :- emptylists(Xss).
headsandtails([[X|Xs]|Xss],[X|Hs],[Xs|Ts]) :- headsandtails(Xss,Hs,Ts).
emptylists([]) :- !.
emptylists([[]|L]) :- emptylists(L).