It shouldn't create a misalignment if you use the snap grid properly, but you may need to mask the second grid in places. Or you could just draw one grid across all, and mask those areas of the grid that lie beyond the structure's walls.

As with most things in CC3+, there isn't just one option for solving issues like this - it's which one you're more comfortable with that typically wins the day.

Economic and wildlife symbols often get left out - and even when the overland styles do include some, they can be quite selective. They're often useful, and more helpful for GMs than simpler dot-type place-markers.

Ruins, and different types of ruin (so you could build up to a ruined city, say). Could include giant statues (like the Sphinx or the Colossus of Rhodes).

Ships, sea monsters, reefs, whirlpools, etc., to decorate the oceans.

Flat-topped mountains (like mesas), volcanoes, lava flows, glaciers.

A few ideas only, but maybe something to spark some further thoughts from yourself, or others here?

If you're finding the mapping a drag, and not really enjoying it, it may be worth considering a broader-brush approach to the city overall - such as the Watabou style, that shows general areas only, with just a few important places highlighted, roads and general layout. Then if you feel so inclined, you could add detailed areas for selected spots as separate maps - that way, you don't need to worry about how the map looks zoomed out, and can pick area sizes to better suit the time and energy you have available for detailed mapping.

As Sue said, what you've shown here looks good in detail, but if it's not inspiring you, it may be worth a rethink, if only for next time.

I like the idea of the individual structures. There are times when it would be nice to have that option with some of the overland styles, so you could have smaller settlements - and indeed even larger ones - with more individual character, especially for smaller area maps (which, to be fair, isn't really what most overland styles are geared for). Other styles work well with just a single set of settlement symbols, however (makes recognising the different types much easier!).

An all-map greyscale RGB Matrix effect usually works fine to convert colour to black and white - that's what I did here with some hex maps, rather longer ago than I'd thought!

The creator of the HighSpace style, Joe Sweeney, did a series of tutorial videos when this was released (so for CC3, not CC3+), which are still available on YouTube. There is a link in the CA70 HighSpace 2 PDF Mapping Guide (there isn't a Guide for Part 1), but it goes to the wrong place. This link though takes you to the right place on the ProFantasy site, where you can download the videos. If you'd prefer to watch them online, they're here instead on YouTube.