Brenno
sFTP is encouraged, yet the wiki articles imply a security risk in enabling Remote Access via SSH.
AFAIK sftp and ssh are different. I'm not aware of any security issues with ssh. You can ssh (using Putty) as a user rather than root and be very limited in what you can do/access, as determined by ssh access permissions granted to the user (seperate permission model than server manager groups). You can use the scp command to copy.
VPN access ..... is a little dicey ..... where specific permissions will govern which files/folders are accessible, but will also have access to all IP nodes behind the SME server
The permission model is governed by Group membership, the use of which should be standard in all sme installations. When correctly setup, a VPN user would have NO access to ibays on the server unless or until they are made a member of the Group that owns the ibay. If you wish to limit access to one ibay for uploading files for a specific website, then you create a unique Group that ONLY your web developer is a member of. They and admin will be the only people who can access that ibay via samba.
Re access to all other hosts (IP's) on the network, this would usually be limited by domain membership. All host access would only be granted to users who have logged into the domain, and basic VPN access does not log a user into the domain. Again a VPN user cannot access hosts(IP's) behind sme unless they have permission to do so.
Typically a VPN user would be a trusted user as VPN access needs to be enabled on a per user basis, they need to firstly be a sme user (with limited access permissions if required), but VPN access needs to be enabled too.
Re giving a user access to an ibay, I see no problem with VPN on a system configured correctly.
You could also use ssh/Putty or WinSCP and login as a user with limited access permissions, which both use the ssh protocol which is known to be secure.
With sftp the ability to see folders is somewhat irrelevant if you don't have permission to access them. There is a suggestion made to use a newer openssh rpm which may fix the chroot jail issue and therefore resolve this problem.
You can use WebDAV as suggested with it's potential bugs.