Spectral hole burning (SHB) and difference fluorescence line narrowing (Delta FLN) are routinely used for investigations of electron-phonon coupling in photosynthetic pigment protein complexes as well as in other amorphous systems at cryogenic temperatures. Nevertheless, the Huang-Rhys factors S, an integral measure of electron-phonon coupling strength, and the phonon spectral densities obtained by SHB and Delta FLN over the past years have differed significantly in the case of certain photosynthetic pigment protein complexes. In this work, the specific properties of both types of line-narrowing spectroscopic techniques that may lead to these discrepancies are critically analyzed by a combined experimental and computational approach, using the CP29 antenna complex of green plants as a suitable model system. We confirm that only Delta FLN at low fluence, by providing access to the homogeneously broadened spectrum, is able to deliver correct S values, while SHB may significantly under- or overestimate them, depending on the burn fluence. We also discuss possible other sources of discrepancies in the literature data, e.g., in the case of LHC II aggregates and correct numerical errors found in some previous records.