Thanks for your reply. He used RedGard waterproofing membrane over HardieBacker.
Tiles have not been installed yet. Regarding spacing, the tile description stated "Built-in lugs create 1/16" grout joints." (See caption at bottom of attached pic). Also, the lugs on the 3"x6" tiles form a "V" shape when viewing cross section. Hope that helps!

Screenshot of the image shown in the Daltile subway tile description.

There is no reason you CANT use spacers. Sometimes in a subway install in say A tub surround or shower i may simply add a 1/16 spacer to gain optimal layout and or yes alot room for poor mfg quality/. 9 times out of 10 we go with mfg intended lug

make my choice on both quality of actual tile and layout optimization.

Do you have enough material to make a test panel? Piece of plywood, you space your way, he spaces his way.

You don't have to worry about the water "leaking through" since grout and tile are not waterproof anyways -- the waterproofing magic actually happens behind it, which is why everyone on bathroom forums harps on "what waterproofing was used". The grout just serves the purpose of binding the tile surface together for sturdiness and for easier cleaning.

You can make your joints whatever size you'd like; for what it's worth, I used the Daltile subways with lugs about 13 years ago and they have held up just fine; I liked the aesthetics of the thinner joint. You will probably want the spacers on hand anyways, there are always little placement situations where the spacers come in handy even if you're largely depending on the lugs.

ETA: oh, I see you're also asking about the Daltile variations in quality that might lead to the lugs being uneven themselves. It's a cheaper tile, so we found that there will be the occasional wonky one, but precisely because they're so cheap, you can sort those out pretty easily without losing a lot of cash. I wouldn't be too concerned about this.