Hello Jesus,
That's an interesting question -- and I understand your motivation regarding trust regions.
Endowing the manifold with a singular "metric" might break too many things in the current theory (it might be interesting to investigate separately.) Another perspective could be the following: you keep your proper metric, but you ask: can I use a singular preconditioner when I solve the trust-region subproblem (TRS)? This is essentially equivalent for your purpose, except "trouble" is confined to that question of the TRS.
Framed as such, it becomes a question of rather general interest, since the TRS lives on a linear space (the tangent space at the current iterate), so it's possible that this was already answered in the classical theory of trust regions. I would start by having a look at the TR bible: the book by Conn, Gould and Toint aptly named Trust Region Methods. Hopefully this will give something.
(There is an obvious difficulty here: if the Hessian or its approximation has a negative eigenvalue along the singular directions of your preconditioner, the TRS no longer has a solution...)
(Note that Manopt allows you to specify a preconditioner, and the trustregions solver will use it inside its tCG function, which is an implementation of the truncated Steighaug-Toint CG method, originally from the GenRTR implementation of Chris Baker et al.)
Best,
Nicolas