Yes in that I remember reading about the square cube law about how in order for something to be that large it would have to be made out of things far more stronger then regular bone or skin. So in away if the square cube law was true a giant monster like that would be very powerful angst military weapons.
I also have a custom monster of my own in this book I'm working on and i do explain how it's digestive system works which allows it to spit it's digestive juices up at it's victims.
The way I understood it is that the support structure mass for a land animal has to increase at a greater rate than its size. So the bones would have to be much stronger as you say. If a blue whale had legs which could support it on land, they would be so large the whale wouldn't be able to move.
I remember reading that if a creature lives in the water it can get as big as it wants to in that the water will help carry it's weight. That is why you can run into 40 foot long Jelly fish and fish that can start out as really tiny babes and grow to over ten feet long. As for the bones in a creature they are only made out of calcium so they are limited to a certain size. But if you have bones made out of different elements some of which may not exist on Earth it could be possible for something to get really big.
As for Godzilla his shape sort of makes sense in how bulky looking he looks in that his tail and his thick legs do help hold him up very well not to mention if his skin and his bones are made out of something that we do not know about he would be very hard to kill. As for Godzilla in the water I think he could be very fast and mobile in the water. Also with this said about being very mobile in the water. I don't think he would like coming out of the ocean to much in that do to his large bulky size he might find it aggravating to come up on the land to to the square cube law putting pressure on his joints or body.
I have a original storyline about a giant monster who is a highly intelligent giant alien bird who accidentally gets stuck on Earth do to her going though some type of interstellar travel experiment for her society. But when she gets stuck on Earth she finds out that she is among humans who she finds out are 20 times smaller then her. She at least has the foresight to avoid crashing though their cities and to resist the temptation to eat them. As for the humans they try to attack her several times do to her huge size and soon find out that unless they want to end up nuking one of their cities or towns. They find it easier to give her lots and lots of food for her huge hunger then to try and fight her do to her body be made out of something different then simple bones.
You have a good explanation there for why Godzilla is so grumpy on land! I didn't go into monster physiology when I did a comics series for G-Fan but I came up with a rationale for giant robots that became a key part of the overall plot.
I did work on three fan fictions with Godzilla and Gargantua in it about 66 Maser Cannon drivers and what their jobs are like. In one of them called Godzilla vs. Articuno. Godzilla gets put into a rage when aliens makes him show up in England and he starts trashing the place. In that one towards the end the main characters get to use a giant robot called the Lord Kanawha.[link] and [link] I'm going to have to up date them and post them here in that I made them several years ago.