.elf and .hex equivalency? (code, eeprom, fuses, and lock bits all in one)
My question is, if the two files are equivalent in case of using them for all-in-one programming. Is there any critical data stripping taking place between elf-to-hex conversion that could affect the actual programming?


Nothing critical, but data stripping does take place. Everything that is in the HEX file is in the ELF file. That is - all the compiled machine code and data.

Basically everything that gets written to the chip is in the HEX file, and the HEX file can be created from what is in the ELF file - ergo the ELF file contains everything that is in the HEX file.

However, not everything that is in the ELF file goes into the HEX file.

The ELF file contains a huge amount more information. Mostly that information is geared towards debugging. There are things like the names and locations of all the symbols in the code - that is, the functions and variables, etc. There are breakdowns of all the assembly instructions grouped by source code file and line number. 

None of that is relevant for the Arduino environment, but when you're using professional tools to do your development you can use them for realtime debugging and tracing of your program while it's running on the real hardware. 

None of that is relevant to putting your program on the chip. It's all used by the PC.