Putting the file into a folder into your document root folder may not present a direct risk (as long as you have your permissions properly set), however in case of an attack which comes locally, i.e. LFI, this means the attacker would be able to either abuse your script locally and read sensitive information regardless of any ACL placed, or write to a file which is executable on the server using a server-side scripting language like php or asp.
Imagine the following scenario:
You have a folder for storing sensitive data in your document root, /var/www/html/sensitivedata and at the same time you have restricted access to this folder using an .htaccess file
index.php is prone to Local file inclusion using the following approach:
index.php?p=filename (even if you use specific extensions there are ways to bypass this, but this is out of scope)
Then an attacker would be able to read your file by accessing the following url:
Of course, the same thing could happen if the directory 'sensitivedata' is outside of the document root, however exposing it publicly defines an additional attack vector, as it is clear to the attacker that the directory exists.
A question that may arise is how would an attacker know that filename.txt exists? This can be done either by bruteforcing or by enumerating the filesystem using any other means the attacker may have found.
In case the attacker found a way to write files to the system, he could write an executable script to /var/www/html/sensitivedata/randomscript.php and then execute it by just visiting https://domain/sensitivedata/randomscript.php which would give provide him with local access to the system and the ability to execute commands, called RCE or Remote Command Execution.
Now having in mind the above scenario, in case your folder is outside of your document root, the attacker wouldn't be able to execute the script he uploaded.
An ACL using htaccess wouldn't present a vulnerability itself, but raises a risk in case the attacker found a way to access the filesystem using a vulnerable web script or by any other means.
Any sensitive data or a folder used as a container to store files, especially when they are being uploaded by the user should be outside of document root and handled with caution. If you need to provide any authenticated users access to read them you should implement a script handling the process instead of providing them with a direct access to your folder/file.