I would say the energy audit is more about the metering side and the authentication of the metering results. In this respect, the Excel spreadsheet may contain a checklist to verify the particular installation or would list the outcome of the metered data. The data in the excel tables is typically downloaded from real-time meters or dataloggers. In both checklist and metered data would be verified (signed-off) by a trustworthy authority.
I would say it is a matter of the level of detail you are looking for in your audit. There are software programs available that simulate the whole building, it's systems and the climate conditions at the site in which the building is set. If that level of detail is required, go with that option. For the "low hanging fruit" this is not usually necessary. If a preliminary assessment of the systems and a comparison with the actual meter readings is needed, excel does it. Or if you want to create a comprehensive analysis tool in excel, by programming cells, that can be done too, if you have the time.
Excel could work properly for example as datasheet where you collect the data you need for build your energy baseline. You can use it for plot data and find correlation too. What you can't do with Excel is the analysis of building performance, you need a dedicated software for it.