Discussions shouldn't be limited in the Sanbox as long as they don't start to be massively tangential.
There is only a small subset of users who frequent the Sandbox and there is rarely any topic in there that starts the kind of heated debates that you sometimes see on the Main site. The amount of people who come across the posts is just vastly different. While there can be a lot of back and forth most of the time it's mostly forth, making the question better with each iteration.
Meta discussions can have longer comment discussions anyway and people visiting the Sandbox are encouraged to leave comments. Normally comments are to ask for clarification of the post, whereas in the Sandbox they are meant to be the main discussion part.
Therefore I wouldn't call the comment section in the Sandbox messy. It's the way it's supposed to be and we shouldn't change anything about that. If anything, flagging comments as "No longer needed" in the Sandbox before the post graduated/was abandoned is adding noise to the moderators and should therefore be discouraged - there are rules in place to ask the mods to remove drafts anyway after a certain time.
We should however try to delete comments that are definitely no longer needed. If you mentioned a few small typos in the beginning for example and the OP fixed those you can remove your comment to reduce the clutter. That's just such a small thing that it's not needed for other people that come across the post, it's just noise. Most of the time it can be valuable for others to read through the discussion so far, but it's also extra work to do and we want to make the Sandbox easier to use for everyone - for the people that need help with their drafts and for the people that want to provide this help.
That's also what the linked discussion is about: making it easier for people who can see deleted posts to use the Sandbox. If a draft is deleted, because it graduated or was abandoned, the comments have served their purpose and can only be seen by the OP that decided to use or ignore those comments already and the people who can see deleted posts and likely don't need to read through long discussions about what is and what isn't on-topic on the Main site or how to format stuff.
All of this of course doesn't apply if something for some reason should get out of hand. This includes heated and very, very long back-and-forth discussions that are only tangential to the question. These should be moved to chat like normal. But this also includes trolls. There were some problems with a troll before, so if you feel that someone is abusing the Sandbox to game the system, for example because the Sandbox encourages discussions or because on Meta you can have more bad, deleted posts before running into question/answer bans or something like that you should of course bring this to the attention of the mods.
It's very rare, but just to be clear in case something like this comes up in the future: while discussions about a specific draft and how to make it on-topic are encouraged the normal rules still apply - it's not a free ticket to sap the time of those people that are trying to help others and to ignore the basic rules of the site.