Signal, I think you are misunderstanding what would happen.
In an extremely rough state, this is what the Sagitarii options would be:
Sagitarii maniple 225 points (4x Sagitarii +1x Tech Priest)
All sagitarii stands may upgrade to mole mortars for X points
A sagitarii maniple may add 0-x additional Rapier units for X points per unit.
A sagitarii maniple may take a minorus for X points.
Basically you can swap out the plasma cannons for sagitarii with mole mortars kind of like how the dreadnought option is for marines. This way you could end up with an entire sagitarii detachment armed with mole mortars (excluding the tech priest) That should fix the issue with the baggage. It'll also allow rapiers to be taken in smaller numbers and hopefully make them a useful option combined with the minorus and regular plasma sagitarii. Also, note that the rapier does have an AP shot as well so taking them wouldn't mess up the "purity". With them getting access to a minorus, you'd even be able to transport the rapiers.
So you'd end up with 4x mole mortar armed sagitarii and 1x tech priest, not 4 regular sagitarii and an additional number of mole moratars. The idea is to turn sagitarii into a single option for a heavy weapons support detachment rather than have sagitarii, mole mortars, and Rapiers as separate things to give more flexibility and again perhaps entice people to try out rapiers and mole mortars.
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That's even close to how they're described in the fiction. They're described in extremely similar terms to the Marjoris vehicles.
Stat wise they are as I described. Fluff wise, no, but the point is why is it so much harder for you to accept that the minorus runs at the speed of dismounted infantry standard because the tech priest can make a vehicle that's similar to the majoris, but smaller, move slightly faster due to less weight and more available power yet you have no issue rationalizing that the corvus pod means the same vehicle taking a pod is an entirely different custom built vehicle that supercharges a completely different existing superheavy to give it 1/3 more speed and suddenly calls it a ordinatus? E&C, you did an awesome job with the lists and I respect your opinion highly, but this is one point that I find your point of view just doesn't make sense on.
The simplest explanation is to just make the critter 15 cm. They aren't as large as the majoris by any stretch and dropping points won't fix the issue with them slowing down an army that's already fairly slow.