In the top-down approach, e.g., Fermi interaction obtained from EW Lagrangian, the loop corrections (using dimensional regularization) and renormalization of $G_F$ are done using the full EW Lagrangian. What happens when we don't have a UV complete theory (which we will never have anyway, in Wilsonian picture, since all QFTs are effective) especially in a bottom-up approach? How do we renormalize the theory with contribution from the irrelevant operators?
In particular, I seem to completely miss the point of relevant and marginal operators. Even the irrelevant operators are confusing to me. If I understand it correctly, all results are to be interpreted as the cutoff $\Lambda\rightarrow\infty$ limit. In the Fermi model, there should be a renormalization of fermion mass running with the dim. reg. parameter $\mu$ coming from the $\frac{G_F}{\Lambda^2}(\bar\psi\psi)^2$ proportional to $\frac{m^3}{\Lambda^2}\log{(\frac{m^2}{\mu^2})}$. This seems to vanish in the limit. There should also be a renormalization of $G_F$ proportional to $\frac{1}{\Lambda^4}$. Which also vanishes.
Should we only consider loop diagrams coming from relevant and marginal operators leaving out the irrelevant operators for tree diagrams only? How can SM, QED etc. be effective, since it has no cutoff scale $\Lambda$ attached to it? If all theories are only effective, shouldn't they only have irrelevant operators since contributions from relevant and marginal operator parts will be there no matter how large $\Lambda$ is?