Both rated and maximum RPM are fairly low on these types of diesel engines and running at/near rated RPM for the PTO shouldn't stress it during break-in as long as the load is sufficient but not greatly excessive.
I don't know about Kubota in particular but most engines get run up to rated RPM right after they come off the assembly line as part of the post-assembly testing so they aren't exactly treated gently. For cars and trucks today, following the break-in schedule is most important for the final drive assembly (rear axle/transaxle) which generates far more heat than normal during the initial few hours of operation. You don't want to run the engine at maximum load and certainly avoid "lugging" it always but especially in those first few hours but otherwise the key part of engine break-in is a reasonable warmup followed by operating it under enough sustained load to properly break in the ring/wall interface and avoiding wet stacking if trying to treat the new engine gently.
And you don't want to force a diesel engine beyond its rated RPM but rated RPM even with smaller diesels is usually in terms of the point where power drops off greatly/AFR becomes too sub-optimal due to air intake/turbo/injector/injection pump limitations instead of the floating valves/bending con rods that comes from significantly exceeding rated maximum RPM for the typical gas engine.
For example the 6.6L Duramax diesel in my GMC pickup has a rated RPM of 3450 under power with the torque peak at 1600 and HP peak at 2800 RPM; beyond 3450 power produced drops so rapidly that it would be counterproductive to run it beyond that RPM in order to achieve a more favorable RPM after an upshift. But the rotating assembly isn't bothered by considerably higher RPM and the ECM allows it to reach 4,800 RPM during engine braking by design.
I would much rather break in a new diesel engine at a point closer to its rated RPM than forcing it to produce too much power at lower RPM which will result in more load on the rotating assembly and cause much higher EGT. If I were mowing really heavy wet grass with a new machine, it would be a double pass with the deck raised on pass one to reduce the load. And given supply chain issues, I suspect more than one new owner has more grass height than they want/expected by the time the new machine arrives
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