13th chords as substitutions

Bass notes and root notes are not the same thing. Any note in a chord can serve as the bass - if it's not the same as the root, the chord is an inversion.

Most extended chords have too many notes to actually all be played at the same time. What's typical is playing four notes at once, sometimes five. So you might voice C13 as C-E-Bb-A... C is the root (which isn't actually required in a voicing), the E (3rd) and Bb (b7) form the tritone that gives it the dominant sound, and the A is the 13th. Lots of other voicings are possible, too.

Chords are named from the root, not the bass. If the chord is in root position then the root and bass note are the same, but otherwise it's the root, not the bass note that gives the chord its name. If the root is C, but your bass player decides to play D, the chord becomes inverted, but its name doesn't change, although it might be shown as C maj13/D

But lets just say theoretically somebody plays the whole chord.

If the bassist plays D it could alter the chord because Cmaj13 has the same notes as Dmin13

C-D-E-F-G-A-B-C Cmaj13 and D-E-F-G-A-B-C the Dmin13 ( remember we are playing them completely although that never happens).

Wouldn't a C maj 13/D be the same notes as a Dmin13 ( not if you only play the C-E-B-A but if you were to play it completely)

This is something that would never happen but Its more of a hypotetical question o.o

But lets just say theoretically somebody plays the whole chord.

If the bassist plays D it could alter the chord because Cmaj13 has the same notes as Dmin13

But they don't have the same root. The bassist playing a D below your chord is exactly the same as you playing D as your lowest note in the C maj13 chord. If you play D as your lowest note, you're playing an inverted C maj13. It can only be Dmin13 if the root is D.
The root is determined by the context. If the progression is 'progressing' along in such a way that C is the obvious root of the chord, then you or the bassist won't change that by adding a chord tone (D) below the chord. You'll be inverting the C maj13 chord, not changing the root.
BUT...
If the context is less clear and when the D is added, we can hear that D is actually the real root, then it means it was never C maj13 in the first place, it was an inverted D min13, and now, with D added in the bass, it's in root position.

Ultimately, all diatonic chords are equivalent if sufficiently extended.

Consider:

C E G B D F A
1 3 5 7 9 11 13

D F A C E G B
1 3 5 7 9 11 13

Guess what -- An extended CMaj7 chord is identical to an extended Dm7 chord.

This is one of the things that makes playing with extended chords so much fun. As long as you stay with diatonic chords, you can do anything and have a good chance of it working. You might have to move off a chord pretty quickly to avoid a significant clash with a melody line, but in jazz even that sounds good if you do it right.

One of my favorite tricks is to play a minor chord off of the 6th of the chord, and to shift it down by a whole step then back again:

Example, over a C7 I'd play:

Amin -- A C E -- which is a C6
Gmin -- G B D -- which is a C9
Amin -- A C E -- back to the 6

The sound of the 6-9-6 motion is really smooth, and by letting the bassist worry about the root on the 9 chord, it provides some great voice leading opportunities. It's even possible to move it by half-steps just to add a bit of passing tension.