The Trojan advice (which is pretty much the same as all battery manufacturers) doesn't take into account how smart the charger is, simply because they have no idea what charger you may be using. Most any decent quality multi-stage smart charger will monitor the battery voltage and amp acceptance and adjust the charge amps accordingly, so no need for concern about amp rate or over-charging. Single stage chargers, though, begin at some initial high amp rate and then let it taper off.
The Charge Rate parameter on the Magnum (and Xantrex too) is poorly named and not the same "rate" that Trojan is talking about. It is actually the Charge Proportion, i.e. the part of the total power that is available for use by the charging function. That's why it is expressed as a percentage rather than an amp limit. It is used with converter/chargers, where the total power available is applied to two functions:
1. Power direct to the 12v distribution bus
2. Power to the battery charger
The Charge Rate determines how much of the total is available for use by the charger. The rest is reserved for direct power to the bus. Limiting it to, say, 60% restricts how much charging can be done, but is not necessary in the vast majority of situations. The Magnum's charge algorithm is smart enough to understand and implement the C/10 optimum charge recommendation and will avoid excessive amp rates.
Using a rate of 100% allows the charger to automatically adjust. In Bill's case,a Charge Rate parameter of 60% still allows the charger up to 30A, so still [barely] enough to use for charging of a 225 AH battery bank. A higher percentage gives the charger more flexibility and may allow a higher amp rate for the first several minutes of charge when the battery bank is very low. However, the charger will quickly reduce the amp rate as the battery charge begins to build up. That's the whole idea behind 3-stage charging.