I think that is a very good question, and I am surprised it doesn't come up more often now that Lifeline says it is OK I even talked to the Lifeline techs about it a few years ago.
I think that the equalizing of AGM batteries is somewhat of a crutch to help battery life if the charging system isn't up to par for the most part. If you start with new AGM batteries and do top line charging on them, equalization shouldn't be needed until the batteries are old and nearly at end of life.
My interpretation of top line charging would be to have all the charging systems base their charging on the measured amps to the batteries at absorption voltage. That would be the .5%C in amps that Lifeline says to use for their batteries or whatever other manufacturers recommend if it is not a crazy high number that some do now to match some of the chargers. It is possible to have all three sources of charging, shore, solar, alternator charge by amps if you take the time and effort to get it all that way. Even having one source by amps, probably shore power or alternator (done manually), and making sure you use that source at least every 7-10 charge cycles, is very good and not all that difficult.
For those with not the best charging setups, they mostly will wind up short charging and not getting the batteries totally full as nearly all the charger manufacturers seem to prefer error to the undercharge side as the wear on the batteries is less than the overcharge side. Repeated undercharging with never getting full all the way will cause the batteries to walk down their capacity over time and that capacity can't be recovered by normal charging. Equalization can recover some or most of that capacity if done soon enough after the short charging. From what Lifeline told me is that careful use of equalization could add significant life to batteries when they are losing capacity regularly from heavy use and/or poor charging. The hard part, I think, is catching the need for an equalization fairly quickly without running capacity tests all the time.
The downside of equalization is that it does do some damage itself in an AGM as it will dry out the electrolyte a bit, so you don't want to do it unless needed. Some manufacturers seem to be adding a mini equalization at the end of their charge cycles, presumably to assure the batteries are full and help recover any lost capacity, but I don't really think doing that every time is the best solution. I would say that you likely will learn how long your batteries can go under normal use before losing capacity and it would be very appropriate to do a short equalize in maybe half that use period as a preventative as damage is almost certainly happening before you can actually see capacity loss easily.
Bottom line though is that equalization should not be needed much or at all if the charging systems are doing the charging well, and you don't kill the batteries to near dead.
With the Magnum and ARC50 remote with BMK, you will be able to set the shore charging to control by amps so no problem at all with that as long as the settings are correct. The built in battery monitor will also allow you to see the amps going to the batteries on the ARC50 (be sure to only use BMK amps screen as the "normal" amp/volt screen is not measured by shunt or accurate) so you can determine and even control manually the charging from your other charging sources like engine or solar, so you will be able to quickly determine how well they are doing.
The Lifeline article in the link you provided is a very good description and much better than the much more vague ones they have had in the past. They are very aware that other manufacturers batteries may or may not be able to handle the same equalization.