Yes and no.

By default, UR points are in separate "buckets" based on the account in which they were earned. So if you have a Freedom and an Ink, you have two buckets which each have a points balance.

However, you can do different things with the points in each bucket. The key difference is transferring points to frequent travel programs (airlines and hotels). Ink Plus/Bold and Sapphire Preferred allow this, but Freedom doesn't.

If you have both a Freedom and an Ink Plus, you can transfer points from your Freedom bucket to your Ink bucket, thus allowing them to be transferred to a frequent travel program.