For me personally, I would buy the NA-5spd. I am not really into body work and so all the body work/retrofitting that is required to equip a manual trans is already done straight from the factory. From a financial perspective, NA-5spd would be cheaper so you could have some leftover cash for future plans which is always a plus.
Most of this is all trade-offs. You have to ask yourself what kind of work you want to do vs avoid, and then ask yourself future plans.
Most likely if you were to buy the TT-Auto, you would invest in the T56F trans kit from grannis + plus the extra mods/retrofitting to support a manual trans, but you have the TT engine as a terrific base. In the TT-AUTO case manual retrofit, If you want "OEM", then it will require you to remove the auto tunnel and spot weld the manual tunnel, seam seal, drill holes for the clutch pedal, etc. If you don't care about "OEM", then I think there are like tran tunnel adapter you can bolt on that comes with the T56F kit. With the NA-5sp, you don't have to perform extra body work to support a manual transmission, but drawback is that you have a NA engine. If your future plans is to boost this thing to oblivion, then you are gonna build the engine regardless if you go NA or TT.
Assuming you have a deep desire for the manual transmission, then in the TT-Auto case, you are gonna swap the auto trans for a manual trans and for the NA-5Spd case, you would swap the trans for a stronger manual trans like the T56F for higher power levels. So either case you are swapping the trans.
Just some things to think about.