Generally I've seen it rules that the overlap needs to cover >50% of the square to affect it. In which case you have the exact same coverage as before. But in this case I'd just rule that we shift the grid 45 degrees so it lines up again and move units to the closest square that aligns. I.e. don't use geometry to try to munchkin.
There's a bunch of grid-based shapes that pertain to the rules of 5e as well if you need that. Also 5e fun fact: a circle or radius affect is going to look like a square since diagonal distance is not accounted for, but in Pf2e it looks closer to an actual circle.
I always houserule that "circles are square", because it's so much quicker and easier. It gets a little extreme when you do it in 3D, but I don't overly care.
(For fun, a double diagonal move of 5 places you at 8.66 from the start, almost 75% further than an orthangol move, but still 5 for game purposes)
This brings us back to zones, a good middle ground. Draw rough map, or great map, and on it mark intresting combat zones. Some are separated with emptiness, others by obstacles.
For example a tavern brawl. Zones could be the Bar, Kitchen, Common Room, Balconies, Private Rooms, Out Front and Out Back.
Fighting on the Balconies could be tight, only one in width and with the risk of being thrown off it into the Commonroom. In the Kitchen there would be fire hazards, improvized weapons, knifes and the Stew. Not to forget other ways to spice things up in there. Around the Bar there would be some cover fighting someone on the other side, bottles to be broken and combatants to glide alond the bar for maximum mental damage.
And so on. Make each zone memorable and with special features. Did I mention drawing it out really helps?
This works for situations where exact positioning isn't too important. When want to have AoE spells, move speed, flanking, and battlefield control, it generally because difficult to ensure that the GM and the players have the same picture of the battlefield. Even just drawing it out roughly can help a lot, but pure theatre of the mind really works best when you only care about distance rather than relative positioning and complex battlefield conditions.
Generally I tell players they need to pick a specific point for the cube so that it exactly fits the grid. It just keeps things more objective, speeds up combat.
I also generally prefer more structure and strict rules for things though.