I think it is worth thinking about primary Maths - as indeed the testing process does in Year 6 - as teaching and assessing a mixture of 'arithmetical fluency' and 'mathematical reasoning'.
To achieve the level of 'arithmetical fluency' required by Year 6, yes, children have to be quick and accurate at completing the standard methods for all 4 operations (as well as other arithmetical processes, including spotting when mental methods are appropriate) for whole numbers and decimals.
To be capable of the level of 'mathematical reasoning' required by Year 6, children do need to have a deep knowledge and understanding of what they are doing, over and above their ability to complete calculations.
Hence the type of 'incrasing challenge' type approaches that i listed in an earlier post - yes, children have to be capable of completing known algorithms at speed (hence continued practice of basic methods as a starting point) but also understand what is going on to the point where they can apply this knowledge to complete missing digit problems, one and two step problems in whole number and decimal contexts, balancing equations etc etc.
So for the IOP, if the only maths that your child is doing is 3 digit + 3 digit arithmetical fluency, then yes, that is an issue. But if they are being moved on from that arithmetical fluency to challenges of understanding, albeit still within 3 digit whole numbers and decimals, then it is almost a non-issue as if the understanding is there then adding extra digits is trivial.
So if I were to encounter in Y5 a child who really understood and had a deep grasp of calculating with 3 digits in context, and capable of answering all the types of problems that probe true understanding, moving them on to 5 or more digits from 3 would be a matter of moments - the first 10 minutes of the first lesson. I'd probably then spend a bit longer on the decimal version - so subtracting 1.9804 from 2000.6 - but tbh both are pretty trivial and quick if the understanding is there from working with numbers with fewer digits.
www.ncetm.org.uk/public/files/23305622/Mastery_Assessment_Y4_Low_Res.pdf may be useful (p12-14 are about addition and subtraction) to see what is meant by 'understanding', and why adding extra digits is not the same as true challenge.