TOML's design is based on the idea that INI was a good format. This was always going to cause problems, as INI was never good, and never a format. In reality, it was hundreds of different formats people decided to use the same file extension for, all with their own incompatible quirks and rarely any ability to identify which variant you were using and therefore which quirks would need to be worked around.

The changes in the third panel were inevitable, as people have data with nested structure that they're going to want to represent, and without significant whitespace, TOML was always going to need some kind of character to delimit nesting.