Imagine you can build your soldiers in a lab somewhere. You can control everything, and you've found a the ideal humanoid form (ignoring potentially better forms here). You could build them in all sizes big and small, but this would also mean that production of weapons and equipment would need to account for various sizes and be more intensive, so using a single size for your super-soldiers would be more ideal.

You could have a few set sizes. Pilots of vehicles and aircraft would likely benefit from being small in size as it would mean they need less space inside the vehicle, but then you would simply have two set standard sizes: "normal" soldiers and "pilot" soldiers that are smaller but all still the same size within their category. For clarity let's say all normal soldiers are 1.8m in size and all pilots 1m in size without any further variation. You can possibly imagine a few more size variants like a heavy duty variant that is larger but that too would be set at a specific height without further variation.

What I want is to have these soldiers greatly differ in size, fir example from 1.5 to 2.5m, but I can't find a good reason. Especially for the kind of large-scale warfare I'm imagining the industrial advantage of building them all one size would be so immense it can hardly be ignored. It would likely need to be in part an evolutionary reason that allows a variable size army to succeed more than one with set sizes.

These soldiers rely for the most part on equipment, so building it into their bodies matching their size requirements is not going to be an option.

The problem with identical clones is they lack diversity. One disease will wipe them all out, there won't be small people able to wriggle through cracks and large people able to apply huge brute strength or tall people able to see further.

If you standardize everything into conformity then you reduce the range of different tasks your teams can perform. Instead you want a mix of different physical types across the range and then let each take the role they are best suited for.

Your methods are helpless against mutation.

After the initial injection of DNA into the egg, one can no longer regulate their biological development outside of nourishment and hormone treatment. This allows possibilities of mutation during cell growth.

A particularly dominant mutation could spread throughout the fetus/embryo and result in a soldier with their own quirks. Every now and then one is born with different eye or hair colours, a slightly greater intellect or, coincidentally, an unusual height.

The mutations should not be too radical 'by default', but they could be amplified as a side-effect of the chemical cocktail used to accelerate growth.

Alternatively, mutation inhibitors may have been invented to reduce the frequency or severity of mutations. These chemicals may be too expensive for extensive use and are reserved for an elite force (an interesting concept).

It may simply not be worth ejecting all non-conforming soldiers due to the cost of fertilising an egg/monitoring it constantly/feeding it until it is born. Therefore the soldiers will have to adapt and be trained for their standard equipment.

I hope this provides some inspiration.

Edit:

Having soldiers of various heights could aid remaining unsuspicious when executing covert operations, since otherwise a soldier of exactly e.g. 1.836m in height would be suspicious and taken aside for inspection at border controls.

In large groups, having soldiers of various heights would aid visibility of a singular position, similar to stages.

Varying heights could aid in combat specialisation, with lower centers of gravity allowing for more athletic maneuvers while taller soldiers could perhaps have more strength or leverage.

Short soldiers would take less space, less food, less material for uniforms and less weight among other things, making them ideal for mechanical deployment, sieges or other forms of long-term semi-isolation.

Taller beings would be better suited as look-outs or for transport purposes, being able to march quicker, wade through deep marshes and step/climb over obstacles more efficiently, but having a high center of gravity would not necessarily be advantageous as far as I can tell.

Weapons come in different size, usually called calibers for fire weapons, specialized on different use cases. I.e. no sane soldier would use a naval cannon to shot an opposing soldier.

Weapons are already produced on industrial scale, yet there are different sizes.

Your soldiers are nothing more than a new type of weapon. Just find the optimal use case for each size.

Different models for different jobs

The ideal infantryman looks nothing like the ideal pilot. The ideal pilot doesn’t necessarily look much like the ideal tank operator. The ideal tank operator certainly doesn’t look much like the ideal medic. An army is full of people who play different roles, and there’s no reason to make them all look the same.

Like father, like son

If you want a fun excuse for this, say that each job role has a ‘blueprint’, based on the most outstanding representative of that role at the time when this super soldier was begun. All the medics are the perfected ‘sons’ of a highly decorated combat medic, etc. This gives you diverse looking troops who are incredibly proud of their lineage.