I don't understand why you would have effloresence if the bathroom has been waterproofed under the tiles, the question is where is the grout drawing salt from? The silicon job isn't great, but can see how hard it would of been to do. I think you won't notice this as much as time goes by.

Get quotes on timber and tile. Tiles can be cheap but the laying is quite expensive. You may be surprised at the cost difference.... it could be quite close so don't discount it all just yet. If you have resale concerns then avoid laminates as they're seen as a cheap choice. For me I'd grit my teeth and pay for a solid timber floor everyday unless in wet areas where I'd use a classic and timeless tile.

Some people prefer the metal tile trims and the black and white ones look great if they match the tiles. The mitred edge is the hardest to get right and most time consuming. it all depends on what you have picked and agreed to. The tiler should have explained either way.

I have a shaker style kitchen and went for a combination of knobs on the doors and pull handles on the drawers and I love the end result! Id go with your last two options, I wouldnt recommend the first two handles you have as they will date more quickly than the others (and also cleaning them would be a hassel)