You are absolutely right. I have been using a NAS and store everything in the NAS from 2018. I download all the files directly to the NAS and I haven't had issues until this week that I installed macOS Sequoia in a new hard drive. I mean downloading from Safari. Firefox and Librewolf have no issues.
As you are saying, Safari downloads the file in a folder of the same name of the file it's downloading and I think I may have some clues and why is happening. Finder in macOS Ventura and also Monterey had quite a bug when renaming files in a network shared folder. Once moved or renamed, Finder was not able to find the file in a while (the time it took no-one knows). If you open the file from a Third party application chances were that you could open the file, even QuickLook would work but Finder was unable to open it, rename it or move it. So I think it's happening again, when in Safari you configure downloads to ask you or even if you set it up to download directly without asking to network because of Safari using Finder internally it creates a Folder with the actual file name, then it renames to .download so it can move the original downloaded file to the parent folder and delete the temp file, and because it's slow once renamed it does not find the renamed folder, so it cannot get inside and move the download original file.
I am going to paste my nsmb.conf I created manually after lot of research because I had a lot off issues when this bugs were happening with a Qnap NAS but not with a TrueNAS server.
Keep in mind that this is for trusted local area network environment where I am just myself.
Probably you should not disable packet signing nor session signing.
One of the biggest issue is Finder's Caching. (Path Finder and other third party managers work way better).
[default]
# Disable NetBIOS
port445=no_netbios
# Disable packet signing
signing_required=no
# Disable SMB session signing
#validate_neg_off=yes
# Enable SMB session signing
validate_neg_off=no
# Disable directory caching
dir_cache_max_cnt=0
dir_cache_max=0
dir_cache_off=yes
# Disable SMB notifications
notify_off=yes
# Lock negotiation to SMB2/3 only
# 7 == 0111 SMB 1/2/3 should be enabled
# 6 == 0110 SMB 2/3 should be enabled
# 4 == 0100 SMB 3 should be enabled
protocol_vers_map=6
# SMB Negotiation (normal, smb1_only, smb2_only, smb3_only)
smb_neg=smb3_only
# Use NTFS streams if supported
streams=yes
# Set hard or soft mount of shares
# Hard mount: a request is issued repeatedly until the request is satisfied.
# Soft mount: tried until completed, the retry limit is met or the timeout limit is met.
soft=yes
# Apple SMB extensions
# ReadDirAttr: This feature changes how macOS handles reads of file metadata stored in
# alternate data stream when listing the contents of large directories. Finder info,
# access rights, and resource fork size are returned more efficiently for the files
# in the directory.
# OsxCopyFile: With the SMB2 protocol, Microsoft implemented server-side optimizations
# when copying files between directories on the file share. The extension introduced by
# Apple ensures that all Apple-specific file metadata is properly copied along with the file
# itself. The copy process is also simplified as it is executed in just one request as
# opposed to splitting the requests into logical chunks which was the case in
# the original feature.
aapl_off=false
# File IDs are legacy compatibility elements for AFP and are not supported by SMB.
file_ids_off=yes
# Disable multi-channel connections and prioritize the wired ethernet connection
mc_prefer_wired=yes
mc_on=no
# Enable multi-channel
#mc_on=yes
But I still have not found a solution to the Safari download issue.