Yes, I still use the master and slave keybinds, mainly because I use the alt+1, shift+1 and ctrl+1 modifiers for separate abilities.
yeah, i also use alt,ctrl,shift for seperate abilities in my macros, even with using the same master- and slavekeys.
This was one of the main reason for me using HKN, as you can us ralt,rctrl,rshift for the ftl-window-identifiers and lalt,lctr,lalt in the macros...

so for example my hunter dps macro looks like this:

/click MacaroonButton12
/castsequence reset=target/lshift Serpent Sting,Null
/cast [mod:lalt] Multi Shot
/castsequence Explosive Shot, Steady Shot, Steady Shot

with my ftl-targeting-and-hold-macro on MacaroonButton12 being:
/stopmacro [harm,nodead]
/assist [mod:ralt, ... (as ftl-mods as usual)

(In my HKN-Script i would add the following for '2' as my dps button:
<ApplyTemplate FTL "2" "2">
<ApplyTemplate FTL "lshift 2" "lshift 2">
<ApplyTemplate FTL "lalt 2" "lalt 2">
but this is better described here: [HotKeyNet] Implementing an FTL quite simple with templates )

If I can find an easy way to quickly switch between the two methods, I'll probably do it.
well, you could use the idea of switching ActionBars combined with the /click in the Macros for this (i do something simmilar to simply chnage between my trash/boss-dps macros).
What I mean is:
Lets say you create a 'paged' bar with macaroon (with only one button), on the first 'page' you create the normale '/assist'-macro on the second the target-and-hold-one (and on the third a focus-based approach for vehicles ;) ). The button should always have the same 'name' so you could simply refer to him in all your dps-macros regardless of which actual 'system' you are using.