I created a cylinder which I remeshed and sculpted some details on one of its sides, when I apply transformations or try to join this of object with another object it gets distorted and sort of inverted. Hoping someone could help with explaining why this happens? Please see video for further info.
You probably have Backface Culling enabled
and your object is scaled to -1 on one or all three axes (two axes won't be a problem): this makes it look like you don't have inverted normals, they look correct but only because the scale is inverted.
If you now apply all transforms, the scale will be reset to 1. In this case it means, the normals get flipped because other than the mesh vertices which simply stay in place, normals have a front and back and inverting the scale makes a difference on them. And with backface culling enabled, the front faces are now invisible and show the rear faces, which are blue because they are pointing inwards.
If you would disable backface culling it will become obvious, because now the front faces are shown in red.