Concerning rectification, I think it depends to what use you are going to put the spectrum. For your own personal use or in a specific study, you just need to do what is required for that application (Which as an extreme example could be all about as accurate as possible wavelength calibration and nothing needed concerning flux calibration if all you wanted to know was the RV) .
The problem comes where you might be uploading data to a general database where you do not know to what use the data is to be put. The rule I apply (which is the philosophy behind the BeSS database) is that you should do all reduction that the user cannot do (eg wavelength calibration, flux calibration by correcting for instrument response) but not steps that the user could do for themselves (eg heliocentric correction, rectification, telluric removal). making sure that the appropriate flags are set in the header.
In this specific case however, If I was uploading this to a database, I would rectify it. To upload it as is including the continuum would be misleading. The reason is that the continuum shape is completely artificial having been made to fit that of a typical star of similar spectral type. For all we know this might bear no resemblance to the actual spectrum. By rectifying it, we are not losing any data, since the continuum shape is not derived from the spectrum and the user should they wish, could add back the continuum shape using their own typical B star spectrum.
Concerning measurements on rectified spectra, EW measurement of absorption lines is no problem as they are measured relative to the continuum. Measurement of emission line strengths is problematic though as the actual flux in the line is usually the important parameter rather than the EW (as in general emission and continuum flux are not related) and measuring the relative strengths of these at different wavelengths (even in relative flux) requires a non rectified accurately flux calibrated spectrum.
Robin