Printed model is not the same dimensions as the CAD version?

I’ve printed the following model using Creality Print 6 and my K1:
https://makerworld.com/en/models/969430-sd-card-storage-holder-w-magnetic-latch-modular#profileId-940749

Assembly guide:

The measurements from the model are:
Top lid height = 3.6mm
Bottom lid height = 3.6mm
Each SD Card tray = 3.25mm
Four SD Card Trays in total = 13mm
End block = 13mm

Thus, the designed height of the top & bottom lids + 4 trays equals 20.2mm.

When I printed the model, it came out with a total height of 21.05mm, over 1mm more than the design. This was with the model fully assembled. I’m using 25mm M3 bolts to keep the model together- the heads of these silver bolts are not the same as the Rounded Hex bolts which I have so the head sits above the top lid instead of inside the recess.

The four trays when printed, have a combined height of 13.55mm. Each tray measures to 3.38mm. These were printed in eSun PLA+ Yellow.
The end block when printed came out as 12.93mm. This was printed in Creality HyperPLA blue.
The whole model was printed on the same day.
Using Creality Print 6.1 with default settings.

The recesses in the bolt design of the model, top and bottom are by design 3.2mm each, thus the distance between the bolt head and the nut is designed to be 20.2mm - (2* 3.2mm) = 13.8mm which should accommodate the stated 16mm bolts which should be used. I tried the 16mm bolts and I cannot get the bolts to engage with the nuts.

It seems to me that the eSun yellow PLA prints bigger than supposed to.
The Creality Hyper+ blue filament seems to be OK and printed very close to the design measurements- thus the End Block of the model being smaller than the combined yellow trays.

How can I fix this?

Images of the printed model:
Front View:


You can see here the front swinging block is not heigh enough as the 4 yellow trays are holding the top and bottom lids further apart than designed.

Side View 01:


You can see the effect of the 4 trays and how much higher they are than the end block and front swinging block, causing the top & bottom lids to flex.

Rear View:


This shows how the end block sits with gaps due again to the height of the 4 yellow trays.

Side View 02:


Shows the gap between the front swinging block and the top & bottom lids.