Colour matching shouldnt be a huge issue. Plenty of suppliers have tons of colours and most retailers can order in the colours you need.

You will not be able to match caulk colours perfectly. They vary batch to batch even if you get the same colour from the same supplier. Existing caulk might also discolour over time and not match new caulk. However, if there are no direct joins, you should get away with doing one separated section, such as around the lip of the tub, in a replacement colour without doing everything else.

As for waterproofing, caulk in bathrooms should basically be a first line of defence. Grout and most tiles are porous and water will get through them. The bulk of the waterproofing should be a membrane under the tiling.

If its just the ends of your caulk that are tipping up, id personally just try sticking them back down again with some glue or whatever. Removing caulk can be easy or very painful, depends on access, thickness, etc.

Putting down a nice bead is also sometimes very easy and sometimes very difficult. If your surfaces meet, then it will be quite easy, but if youre filling in a 10mm gap with caulk, you will have a very shit time.

The easiest process ive found is to have some paper towels or rags ready, lay the bead, spray the area with soapy water, spray your finger with soapy water, and then shape the bead with your finger. Clean the excess onto a rag, and continue. If you dont use soapy water, you will have a shit time cleaning up. A very shit time.

Tldr this is not a big problem and you can choose to leave it or repair it for cosmetic purposes, the real waterproofing should be under the tiles.