It's not exactly that input channels 5 & 6 are totally out of the picture...
when recording in DIRECT mode.
On the 424mkIII, even though the recorder is set & recording in direct mode, channels 5 & 6 may be brought up on the L/R buss and monitor with everything else, however, it will not route 5/6 to tape.
And, it's not that you
can't use direct and buss mode recording simultaneously, but your direct tracks will record direct from the numbered input, and tracks set to buss mode recording would pick up an uneven mishmash of all the channels on the buss, 1-6, including your direct channels.
In other words, not to repeat myself too much, but on the 424mkIII there's no facility for muting the direct-mode channels from the L/R buss. Therefore, plan as you may, but using direct mode and buss mode recording simultaneosly would not necessarily yield your optimum signal routing or proper isolation of tracks or inputs.
For doing what I think you had envisioned, signal routing-wise, you're in 246-ville, with it's 6 inputs independently routing to any of 4-BUSSES. The 246's 4-buss operation is a superior mixer solution to what the 424mkIII offers in DIRECT or 2-BUSS recording.
In your case,... assuming a bit at this point,... you may want to get a 4-buss outboard mixer with 8 inputs, like
the Tascam M30 or 300 series mixer, with which you may route any of 8 or more inputs to 4-busses, AND THEN patch the 4-BUSS OUTS of the M30 to the 424mkIII's INPUTS 1-4, and record in DIRECT MODE. With an M30 and 424mkIII, as described, you're accomplishing what the 246 does in one package.
Just some afterthoughts and advice. I don't wanna seem like I'm upselling you. Good luck.