Given New Macross flagships as colony guardians, and not being designed to have a main gun equal or exceed SDF-1 doesn't make sense.
Anyway, I think the ability to destroy several ships with a single shot depends on the spread of the beam. The larger the spread, less concentrated, good for "carpet bombing" effect to clear enemy mechas, smaller vessels etc. For concentrated shots, probably meant to take out larger capital ships as seen in the last episode of SDFM when the SDF-1 fired a concentrated salvo on Kyron's crippled poo.
As for SDF-1 main cannon wiping out 2 Zentran ships when they approached Earth, I think they these vessels were probably scout type, hence smaller size.