2.1L vs. 2.0L is not really about turbo sizing. It's about putting the torque band where you want it.
2.1L will shift your powerband left from the 2.0L. More torque off-boost, boost will happen sooner, and very high RPM capability will be slightly worse. However on the EJ205, high RPM performance is non-existant due to the heads, so you end up in a win-win on an EJ205. You gain on the low and give up nothing on the high end since the heads are the limiting factor.
My opinion is that the 2.1L is just a better shortblock match to the stock EJ205 heads and it's always a better option for a street engine... it's just a matter of whether the extra cost is worth it to you.
A moderate turbo actually works to the strengths of the 2.1L with stock EJ205 heads. I'm not sure a TD04 would be great for it, but it would work. The 5MT might not like that pairing so much. vf39- GT3071 ish are good sizes to match with stock heads.
You can always start with your vf39, then move up if you feel like it (or funds allow).