Gotta love the consumer keyboardists who have never held a trowel in their life. LOL! Spacers won’t work as intended when the floor isn’t perfectly flat. Especially with hex. It has 6 sides, not 4. Most people couldn’t get it to space out correctly on their kitchen table, much less a floor. Tile has to follow the contours, and that means narrow in some spots and wider in other. Normal old floors aren’t perfectly flat. And many times can not be made that way within the constraints of an apartment environment. Not unless the downstairs neighbor will let you in to completely destroy their ceiling and mess up their place too. The goal is to do the best that the site conditions—and budget—allow. 4K of prep work would probably get that pretty flat. And create a height difference at a threshold to another room. That’s the difference between the real world of budget installs and all of the things photographed on Houzz. People think that these photos are “normal”. It isn’t normal. It’s well above average, super high end work, with a super high end budget. Money produced all of these inspiration images. You want that level? Hire the most expensive person that you can find. Then find out who trained him and hire them. There’s been plenty of well done jobs where the grout color was off. Sometimes there’s just a bad batch. Sometimes it is over washed. It isn’t automatically anyone’s “fault”. It’s unproductive to take such an adversarial outlook as well. Focus on a solution. That would be a grout colorant. The installer should be willing to apply it if the customer buys it. Then live your life and be happy!

If you have a curb, you will have the cracks develop there, too. and where the walls meet the floor. Anywhere where two different materials meet or where one surface meets another that is in a different direction (known as "change of plane"). My contractor still grouts such places, too. But I did a solid surface shower that he could not do wrong. I am keeping an eye on the place where the floor meets the shower pan, all other places are in dry areas. So there it is just cosmetic. I would guess that water can get behind your tile with those cracks. If properly waterproofed it is fine, but if not, I would get to this as soon as you can. A lot of shower builders do not use waterproofing, even though it is now required. If you do a search on this forum for "Shower waterproof," you can see many discussions about it and learn what is and is not waterproof. (Redguard yes, Durock no, for instance.)

Grout colorants come in several colors. You can keep it the same, or change it. Your choice. With your grout joints not being consistent, I'd recommend staying with a color close to the tile. The closer you stay to the color of the existing tile, the more the grout lines will visually recede and blend with the tile.

looks like pigment issues and or efflorescense. Id suggest an epoxy grout colorant , black grout is always a gamble. Id lean on tech support from the grout/sealer MFG to make sure the sealer is stripped first for proper bond if needed.