Can I safely asume that links between subsites on a subdirectories based multisite will be treated as internal links within a single site by Google?

[PabloCulebras]

I am building a multisite network based in subdirectories (of the mainsite.com/site1 kind)  where the main site is like a company site, and subsites are focused on brands or projects of that company. There will be links back and forth from the main site and the subsites, as if subsites were just categories or pages within the main site (they are hosted in subfolders of the main domain, after all).

Now, Google's John Mueller has said:

<<as far="" as="" their="" url="" structure="" is concerned,="" subdirectories="" are="" no="" different="" from="" pages="" and="" subpages="" on="" your="" main="" site.="" google="" will="" do="" its="" best="" to="" identify="" where="" sites="" separate="" using="" but="" the="" is="" same="" for="" a="" single="" site,="" you="" should="" assume="" that="" seo="" purposes,="" network="" be="" treated="" one="">></as>

This sounds fine to me, except for the part "Google will do its best to identify where sites are separate", because then, if Google establishes that my multisite structure is actually a collection of different sites, links between subsites and mainsite would be considered backlinks between my own sites, which could be therefore considered a link wheel, that is, a kind of linking structure Google doesn't like. How can I make sure that Google understand my multisite as a unique site?

P.S. - The reason I chose this multisite structure, instead of hosting brands in categories of the main site, is that if I use the subdirectories based multisite feature I will be able to map a TLD domain to any of my brands (subsites) whenever I'd choose to give that brand a more distinct profile, as if it really was a different website.

[Chris.Menke]

"Can I safely asume that links between subsites on a subdirectories based multisite will be treated as internal links within a single site by Google?"

At best.

Unless they're otherwise straight-up  professional links with zero spam intention, I wouldn't use them.

[PabloCulebras]

Hi Chris, thanks for your answer. I don't have any spam intention, those links will help to navigate from the main site to the subsites, which, being hosted in subfolders of the main site, will have the URL mainsite.com/subsite1; that is, as if they were categories. The point is, I want the whole network based on subdirectories to work as a single site based on categories...

I could do the same using categories on a single site, but hosting it on a subfolder of the main site allows me to transform it on a completely different site simply by making a TLD mapping to its folder. Obviously, making this domain mapping operation would transform "internal" links between subsite and main site into external links, but I'd have the option of removing them prior to making the domain mapping.