Hi first of all, it is really really common for babies to hate being in the car seat at this age, and doesn't necessarily mean there is anything wrong. They just don't understand why they have to be restrained, it probably feels weird to be bumped and moved around, they often can't see you and again they can't understand why. It is a phase and it often gets better on its own. I used to find singing to my DC helped a lot, maybe it helped reassure them I was still there? We did nursery rhymes on repeat so you don't even have to think.
If you wouldn't find it a distraction, it's often possible to fit an infant carrier with seatbelt on the front seat, if you can disable the passenger airbag, this sometimes helps. You MUST disable the airbag to put a rear facing seat here, by law.
Secondly, the fit you're getting here is fairly standard for a baby with a newborn insert in a seat which is primarily designed for older children. While I don't think it's likely to be uncomfortable as such, it can look awkward which is why most infant carriers only have the 3-point harness. The fit here is fine - you could possibly tug the shoulder straps down slightly and tighten a teeny bit more, but it is safe and appropriate. The reason it looks strange at the crotch strap is that the insert is chunky and is pushing the baby's bum up underneath the strap, as a way to shorten it to fit them better, otherwise the buckle would be too high on their tummy. This is perfectly safe and various newborn inserts work this way.
Usually an infant carrier will give you the best and perhaps most comfortable fit for a baby this age, because it's more designed for their age and size. At 11 weeks, it might be you can take the newborn insert out of the Pebble 360. The guidance is 60cm, but it's OK to remove it slightly sooner if the baby seems more comfy without, or keep it slightly longer if they are more comfy with. Your baby is likely to be over 60cm when they are starting to transition to 3-6 month clothing.
In the Pearl 360 which you have, you say that it's suitable from birth with the insert you have, I can also see from the picture that you do have the additional newborn insert in that seat. This also is up to 60cm guidance, so it could be that you can also try baby in the Pearl without the newborn insert. From what I know of Maxi Cosi seats, I suspect that you won't get a very good fit unfortunately, as their newborn inserts for these 0-4 years seats are huge and chunky, but can't be adjusted past the lowest headrest position, so there's a fairly extended period of several months where the baby is too big for the newborn insert but too small to safely fit in the seat without it, and the recline doesn't go back enough to support them either. Babies can cope with a bit less recline once they can hold up their head and sit with assistance, around 4-6 months old. Maxi Cosi used to sell a comfort insert, which was quite a good fit for that in between bit, but it looks like they don't do it any more so it might not be suitable for use with this model anyway. With other brands of seat, the newborn or infant insert is often up to ~87cm or 13kg and can be used with more than one headrest position - I find this much better. I don't know why Maxi Cosi don't offer that.
Without the newborn insert, the baby is too small if their shoulders are lower than the straps on the lowest headrest setting, if they have more than about 1-2cm gap between their hips and the edge of the seat, if there is a gap between the front of their pelvis/nappy and the crotch strap, if they slide or curl down to one side in the seat, or if they seem to struggle to support their head properly. Any one of these means they still need an insert to fit safely, even if they are too big for the newborn insert. (As said - often a gap with Maxi Cosi seats).