1. If you cut into it, it'll lose it's strength.
2. The metal means it has huge issues with condensation so it needs to be insulated in a particular way to make them safe long term.
3. It is almost always better to build a new structure instead.

I half built one with no building experience, I'm a welder so handy enough but never installed windows or any kitchen or bathroom stuff before, got it up to a semi liveable stage, tv, lights, kitchen, half a bathroom and lived in it for 2 years, even brought the baby home to it, Looking back, did the job, was pretty rough but got us where we needed to be

Low natural height gets more fucky with duct work and other stuff typically run through ceilings. You have to insulate which eats into usable space (plus utilities, plumbing, etc.), if you go double wide to have more space, you have to reinforce it because otherwise it'll start to deflect as its lost its base shape.

If you're doing it to save money, all that stuff adds up real fast.

Thanks to everyone. Great brains trust here and lots of experience. The overall understanding I've received is that container homes are not a great idea unless you have the right set of knowledge, skills and equipment (or people who can do the work for you professionally). And, the resulting space may not be great plus there can be additional structural problems down the track. So thank you again for all your comments. I've learnt a lot and the decision is clear for me now. A container home is not the ideal 'granny flat' for me.