You can also chop the feet in the industrial thing (right), and then both more or less fit into the 40mm bases. Or also deform a bit the rocks in the other (left), to avoid the side "spikes", or chop most of rocks (make it 5-10mm shorter, less out of the ground, ie, not print the bottom layers; after all that can be modelled with some rocks and sand) and leave only the labyrinth pattern above. From where are there?
If you want to be fully ITS legal objectives should be on a 40mm base. Outside of that, a 55mm objective will mean troopers have to travel a slightly shorter distance to get to the objective, but as long as they're all the same size neither player will get an advantage, and the distance is short enough (7.5mm) that it won't meaningfully affect the number of orders needed most of the time.
Kind of a minor thing, but worth considering is the table. With setting up the table for multiple missions terrain may need to be adjusted more to accommodate the larger base sizes.
It wouldn't affect gameplay much but in my opinion you're better off following the rules even if they are arbitrary. In addition to the base being closer as mentioned by @colbrook the increased surface area would mean it might change the way multiple units could interact with or touch the base. For example, if you're using the antenna marker as the Biotechvore Antennas in the "Panic Room" scenario, a 55mm base can accommodate more units clustered around it for protection. It seems to me that if you're going to go to the trouble to 3d print and paint objectives, you might as well make them fully playable/legal - especially since scaling the models by a few % takes literally seconds in the slicer app. What if your opponent has their own antennas they want to play with and they're 40mm and you end up with 55mm antennas on your side of the board and 40mm antennas on theirs? Whether or not it actually affects gameplay in a significant way (hard to tell) the perception might be that you're bending the rules to your advantage and it could color the interaction.
Sorry about the misunderstanding. My impression is that generally people are not customizing objective markers per-mission, but rather per-type (e.g. antenna, tech coffin, console) - so I had no idea you would literally be making different markers to represent all of the potential iterations of a given type of marker . For me personally, I don't see any advantage or disadvantage to sizing objectives differently, so I'd just assume make markers that match the size the game suggests - it's frankly odd to me that the game even includes 25mm based "beacons" as opposed to 40mm "antennas" in the first place, but I play it as it is in the rules because I figure that's the most straightforward option and the least likely for someone else to object to. I'd assume someone who is a stickler about a true scale build of an S3 Biotechvore Antenna would also very much care about an antenna token being 40mm, because while it's not clear what the actual height is in the rules, the base size is objectively (pun intended) 40mm, but to each their own. Obviously do whatever you want to do. And when I say "trouble" I just mean that if I'm spending time and effort making something, I want it to have the most utility, and for me and the people I play with, 40mm objective markers have more potential utility than 55mm because I think 100% of people would agree to use my 40mm markers and that allows me to get them to the table and enjoy them the maximum amount. I am absolutley not averse to building scenery and have multiple buildings and objective markers that I'm plugging away at in my 3D printing queue currently, because I also love making and painting scenery. Honestly I think it would be cool if objectives had even more table presence. If the game allowed blast-template sized objectives, I'd absolutely be building custom stuff.
