Not sure what a "TTL" is. TTL is an obsolete logic series which used voltages which are not quite compatible with CMOS which is what these chips employ.
If you are referring to the USB-to-serial interface, that is required to communicate with the ATmega328 chip such as when uploading a "sketch". Nothing whatsoever to do with "TTL". The 32U4 however uses its own USB interface and an entirely different bootloader.
R28 and R29 in your circuit are meaningless; there is no need whatsoever to be critical about the value of the series resistor, 200 Ohms is perfectly fine as is 300 Ohms or in fact, 470 - whatever you have 200 Ohms or above within a couple of "k".
Putting it all together in this fashion can be regarded as "creative head-banging" - makes you feel you are doing something but entirely impractical.
I used ATmega8 / 88/128 chips on my own. As a programmer I use Arduino Nano and I do not put a bootloader on the chips but only set fuse bits and then upload the program I need.