Quick backstory. First off, I do all of my own bike maintenance, repair and builds.
My wife and I have a Curtlo custom mountain tandem that we've been running on the road. I'm swapping out the Velocity Dyad rims to something suited for mountain tires. We originally wanted to get some road time on it to get used to how it shifts, flexes and generally feels.
Components are...
Onyx 36H hubs <-- These are rock solid hubs, especially with the Sprag clutch in the rear.
36H 29" Sun Ringle Rhyno Lite XL rims. <-- we have similar ones on our road tandem and they've been fantastic. Never have to touch them even after potholes.
DT SWISS ALPINE III Black Spokes 15/13/14 <-- Recommended by Swiss for heavy load bikes.

I strung the wheels 3x and did an initial truing. Side to side was very good and ovality(whatever it is called) was very good too..
For initial truing, I don't pay attention to tension rather I want to ensure that the rim is true and as close to a circle as possible.
I use a Park tension tool with their chart and their online app to help keep things in perspective. Small adhesive dot stickers on the rim also work very well for keeping spoke pairs easily identified.

The front hub flanges are 21mm (disc side) and 34mm off center. Obviously the 21mm side will run a higher tension.
I brought the disc side spokes to 21 (105 KGF according to the Park chart) and brought the non disc side up to 16 or so. As I trued the wheel, I kept the disc side tensions as close to 21 as I could and allowed the non disc side to vary to keep the wheel in true. I know that it is a balancing act but I believe that tension is one of the most important aspects of a good wheel build.

Where I need some guidance...
The wheel was true, tension on one side was equally balanced and the other side varied a bit. It was no longer a circle and had some areas that ran low.
I went through and relieved the tension on 3 spoke pairs in the lowest area expecting the spokes on both sides to increase tension but expecting the rim to come back into shape. It did a bit but not as much as I had hoped. How do you handle getting low spots to conform to the circle?

I plan on dropping all tensions back down and starting again with bringing the disc side to 16 or so, truing it side to side and in a circle and then increasing tension a few points to see what happens.

Compromise.

Building a wheel is a compromise, unless you happen to have a perfectly drilled hub, and perfectly round rim. The first is fairly easy to obtain; the latter, difficult...especially with less expensive metal rims.

You can make a choice, then--do you want a
-perfectly balanced wheel in terms of tension that might be slightly out of true/round?
-a wheel that prizes roundness over lateral trueness, while still holding even tensions to a higher standard?
-the inverse of the above?
-a wheel that ranks trueness/roundness above perfectly equal tension?

In my opinion, tension that varies on some spokes (not the average, mind you) by 5-10 kgfcm is not an issue.

Getting the wheel radially true is a LOT trickier than side-to-side truing.

My method is to work at keeping the rim round as I bring the tension up.
1. After lacing the wheel, I stick a thumb nail into the last spoke thread and twist the nipple from the inside of the rim until my nail bottoms against the nipple. That starts all of the spokes at about the same effective length.
2. From that point on, I count turns as I bring the wheel sloooowly up to tension. I start with maybe a full turn all the way around, then hang turns, then less. Never tighten a nipple more than you're sure you can do all the way around.
3. Only after I get the wheel close to full tension do I worry about trueness. Any truing I do is by tightening and loosening opposing pairs of spokes an equal amount.

That's not the fastest way to tension and true a wheel, but it's how I do it. I once built a wheel for my tandem this way that, after bringing the spokes up to final tension, took absolutely no truing at all. I was stoked.

One of those hand crank screw drivers , used to count turns (full or half), of the Nip, so as to bring the tension up equally , and keep it close to round..

I have one of those, I just never could bring myself to trust it completely. Hence the thumbnail trick.

Some rims plain have hop. What you are doing is completely normal and standard. A few suggestions.

Repeated cycles of tensioning, de-tensioning, then tensioning all over again will often move even stubborn rims with significant hop. This is a slow way to work. But it usually works.

Measure the hop. Always good to have some numbers, now and for future builds. If the hop is 0.5mm or less you are done. That much hop can look enormous against the indicator and when the wheel is otherwise straight. But it is nothing. OTOH if you have done a mostly competent build and the hop is 2mm that is a bum rim and it can be returned. In between those two points it's more problematic.

You can always get hop out with some persuasion. Like with a hammer. I slacken some spokes and use the tension meter to discover how heavy a blow it takes to move that rim. Persuasion should not be necessary on a new rim. But you could.

Sun's recommendation for max tension is low. I just don't believe it. Some lawyer told them to do that. If you follow my advice you do so at your own risk and you are a fool if you take much advice over the internet. But I would tension to 23 and would not ride the looser side with only 16. If you like you could use higher tensions just for building, persuading, and then loosen them before riding. Setting the rim to higher tension will make the rim move more positively when you reduce tension at the hop. If your LBS has any you might try checking Sun's own builds. I'd bet they exceed 110kgpf routinely. I have confirmed as much with other brands but not with Sun.

I work on getting the wheel radially true with a little work on the lateral. As the tension comes up I work on both. Then I bring up the tension and center the rim.