Not trying to complicate your life, here. Rather, it seemed from your description that you run the genset every day anyway, so the thought was that you almost certainly have enough power left over to run a healthy-sized battery charger for those two hours, so why not take advantage of it?
Two things about the Iota's.
1. They are not approved for marine use. However, when fitted with the IQ-4 accessory ($15) they are VERY good multi-stage chargers for the money, and there's a full line of them from about 15A to 90A capacity. I have two of them, one on my boat and one at home, both maintaining a bank of Trojan T-105 batteries. They have run 24/7 for at least five years. I've installed a bunch of them on customer's boats as well. I don't think the lack of marine certification is a big deal, especially if you have a diesel boat. I've talked to Iota engineers and they say there's really nothing to worry about; under normal conditions, there's no spark generation. But, fact remains, they're not marine rated and the marine business is such a tiny part of Iota's business (which is mostly solar and industrial) that they're unlikely to seek such certification anytime soon.
2. You're correct: the Iota's do not have a true equalization cycle; what they call "equalization" really isn't...it's only a high absorption voltage. One strategy might be to use an Iota to pump as much power back into the house batteries as possible with the genset while you're cruising and use your existing charger -- if it has an equalization cycle -- for equalizing periodically when at dockside.
One very nice thing about the Iota's is that they'll take "dirty power" from generators in stride. My 55A DLS-55/IQ4 model runs just fine on my little NextGen generator which has a very dirty output until loaded while my high-end Victron MultiPlus won't even take the genset's output until I load it down!
No matter. You can still find marine-rated top notch chargers for around $500 or less, though. Again, the Sterling and ProMariner Ultra series are about the best ones out there for the money these days, and they DO have a true equalization cycle, and are programmable.
These come in sizes up to 60A. Here's a 50A model for $459. These can also be fitted with a remote control panel if you need that.
Sterling Power Pro Charge Ultra 12V 50A Marine Battery Charger 3 Banks | eBay
MaineSail has an excellent tutorial on his website re: installing one of these. I've thoroughly tested them in my shop, and have installed several on client's boats....they are really wonderful chargers. One very nice feature if you plan to go abroad is that they'll take "worldwide power", i.e., you can plug them into 240VAC 50 cycle current and they'll handle it just fine.