My 2 cents:
Imagine Situation A and B, where A is you having the domain and webhost done by one company, and B is having a seperate registrar to your host. I will refer to these situations in the following points.
1) Your hosting account gets hacked.
In Situation A, If your hosting is hacked, your domain is hacked. You essentially can't reclaim your site.
In Situation B, If your hosting is hacked, your domain is still safe, because it's a seperate service. You could fairly easily move hosting and just point your domain to the new host without much fuss.
2) Cloudflare and "reverse proxies"
In future, you may decide to install Cloudflare or some other "reverse proxy". This allows for DDoS protection, content caching (making your bandwidth smaller and your site faster) and a lot more.
In situation A, 99% of the time you can't do this, or the hosting provider makes it really hard to find the right settings.
In situation B, it's super easy. Cloudflare can even guide you through the process.
3) You want to move host, perhaps for a better deal or better speed.
In Situation A, that's practically impossible. Obviously the hosting company doesn't want you to leave their hosting, so they'll make it super hard for you.
In Situation B, that's easy. Simply change the domain's nameservers and/or DNS settings.
A few other reasons to choose situation B:
- It's often cheaper
- You can get WHOIS protection on registrars, that you may not get with normal hosting companies.
There are so many more reasons, so definitely choose a seperate registrar.