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@MielSharf: Could you please let us know on which page of Woess' article your claim is mentioned (or is used)? For upper central series is true. As every f.g. nilpotent group has a torsion-free nilpotent subgroup of finite index.
@YCor: Thanks. It is also easy to prove the non-existence of such torsion-free groups if they satisfy unique product property. In the meanwhile, if such group exists the size of $B$ must be even.
My last comment: So we have in hand a torsion-free non-left orderable group defining by two generators and two relations. So the group may have Unique Product property?! If not, we have also a surprising group.
@IanAgol: For any torsion-free non-left-orderable factor $B_3/N$ of $B_3$, we know that $N$ must be a free subgroup of $B_3$ such that $N\cap Z(B_3)=1$. It is a necessary condition. So it does not seem (or at least surprising) one can define a torsion-free non-left-orderable factor of $B_3$ with finitely many relations.
@IanAgol: Sorry to ask further. You mean that to define $\pi_1(S_r^3(T))$ one needs only 2 relations (one of Braid group $B_3$ i.e. $xyx=yxy$ and another one, that you explain above) or the relation you gave is a series of relations. I can ask it as a new question.