To get the most out of IS Boxer, you'd want to run with Keymaps on and Repeater off, as your default setting. Mapping everything is a good idea. Keymaps can be as simple as direct broadcast, sending the trigger hotkey to every window, but they can do a whole lot more too.

If both Repeater and Keymaps are on, anything which is a hotkey for a Keymap does whatever the Keymap has been configured to do, and is not broadcast 1:1, like the other keys.

I don't use Alt Shift F12, so am not sure what you're referring to. I have noticed if I turn strobe follow on, then switch toons, it still wants to strobe follow whoever the hot toon was, when I switched. However, if strobe is off and you switch, it should do whatever you configured during the wizard set up. And you can change your choice by going to Character Sets (top pane), clicking on a character set, then on the left pane click on the numbers under Slots.

My follow settings are:
(Checked) When I switch to this character.
(Selected) Do this mapped key.
Keymap = Control
Mapped Key = Follow/Jamba Master

This means, when Keymaps are on -- switching to a new toon has the others auto follow the new toon. I can disable the auto follow by turning keymaps off, and then doing the switch.

With FTL, IS Boxer knows who the leader is, and with Jamba it should automatically set the correct follow for you.

You'll probably still need Focus for vehicles. Enter the vehicle, /Focus Party1 (or /Focus ToonName) and then /Follow Focus.

But as far as normal movement goes, you don't need Focus at all.

If I want strobe to turn on, I have to do so manually. And then turn it off manually as well.

And the targeting is automatic too, via the FTL. You can use macro's just fine, but don't need any form of assist in a macro. I still use things like:
/cast [help] Renew; [help, target=targettarget] Renew... but don't need any type of assist for offensive spells, the FTL does it for us.