We consider a metrology scenario in which qubit-like probes are used to sense an external field that affects their energy splitting in a linear fashion. Following the frequency estimation approach in which one optimizes the state and sensing time of the probes to maximize the sensitivity, we provide a systematic study of the attainable precision under the impact of noise originating from independent bosonic baths. Specifically, we invoke an explicit microscopic derivation of the probe dynamics using the spin-boson model with weak coupling of arbitrary geometry. We clarify how the secular approximation leads to a phase-covariant (PC) dynamics, where the noise terms commute with the field Hamiltonian, while the inclusion of non-secular contributions breaks the PC. Moreover, unless one restricts to a particular (i.e., Ohmic) spectral density of the bath modes, the noise terms may contain relevant information about the frequency to be estimated. Thus, by considering general evolutions of a single probe, we study regimes in which these two effects have a non-negligible impact on the achievable precision. We then consider baths of Ohmic spectral density yet fully accounting for the lack of PC, in order to characterize the ultimate attainable scaling of precision when N probes are used in parallel. Crucially, we show that beyond the semigroup (Lindbladian) regime the Zeno limit imposing the 1/N 3/2 scaling of the mean squared error, recently derived assuming PC, generalises to any dynamics of the probes, unless the latter are coupled to the baths in the direction perfectly transversal to the frequency encoding-when a novel scaling of 1/N 7/4 arises. As our microscopic approach covers all classes of dissipative dynamics, from semigroup to non-Markovian ones (each of them potentially non-phase-covariant), it provides an exhaustive picture, in which all the different asymptotic scalings of precision naturally emerge.