In terms of Zoho One apps, our business operations mostly centre on using Inventory / Books.  Back in the beginning of our time using Zoho, when things were a bit smaller scale, I thought we might be able to run it all under one subscription, by doing such things as disabling the logo and organisation name and addresses, creating separate templates for all documents relating to each business and associating them, using reporting tags in Books so that we could run separate P&Ls for each business etc etc etc ....

For the most part though, it has worked out ok,  keeping the Inventory / Books separate for each business and then combining the figures when it comes to BAS tax time etc. (as, of course, one company means ONE entitiy in the eyes of the Tax Office). 

It did mean we lost the ability to do certain things like transfer stock between the two businesses, ie by having each one as a 'warehouse' under the one subscription, but we are able to fairly easily work around this by using inventory adjustments at each end instead. 

HOWEVER, the main issue that lingers is on the communications side.  We use the Workplace apps, Mail, Cliq etc within the businesses.  With Cliq as an example, it's ok if I am at my computer, because I have all the accounts open as described above, therefore I can receive / see all messages intended for me.  BUT, on my mobile phone app, because I can only be logged in to one of the Orgs at once, I'm only able to receive messages from one half of my employees!  (Depending which business's Org I am logged in to.)

And because we are one company, there are times when it would be beneficial for users in one of the businesses to be able to directly message users in the other business.  But the way it is at present they are two separate 'silos'.  

Sometimes, I wonder if it would be better to set up a separate 'company-wide' Workplace subscription and we all use that instead of / over the top of Workplace associated with the separate Zoho One Org's but I suspect that could lead to its own set of problems.