How does this affect SEO?
Foobars it.
How to notify Google about this?
You can't.
This will likely create confusion to some users, what do you think?
Absolutely!
Should the site be redone again using just one domain only? given the fact that the company is just starting out in a competitive niche.
Absolutely!
TL;DNR
Your developer is not only wrong but nuts too! Make it one domain. There is no such thing as too big for a domain. Not only is he seriously confusing the companies brand, he is seriously confusing the companies customers. That is, if they come by. You are leaving huge potential on the table. How much? Who can say other than to say what you are doing now is catastrophic. Catastrophic enough to be too long to address on this Q&A format.
Here is my experience.
I am a landlord and have occasion to advertise a vacancy. This makes sense especially when you consider that affluence is decidedly separated by how people shop for a place to live. Many sites are owned by companies that are sometimes owned by another parent company. What was common amongst then was the listing site and company site were separate. If I were to go to the listing site, it becomes difficult to know who the company is and whether or not I trust them. Often, there is a sign up without pricing or much of a clue who I am dealing with. Even where this is clearer, it is not clear enough. So who did I chose? The one company that was open with who they are by having one site for all listings and company information. Even then, that is an up hill battle when I can simply put up a web site and be found in search far easier than the top brands who are not doing enough to brand their sites and diluted their efforts. One simple site out performs them all. Are you getting my point?
Real estate company sites are notoriously poor. In 3 months and $70 per month one site returned two scammer inquiries where my site returned several qualified candidates in just a few days. There are many reasons for this. Far too many to list here. But please take it from me, the comments of the developer is way off point if you want a site that performs well in search. Otherwise, the most you can do is mediocre.
Lets look at this logically.
You have examplelistingsite.com and examplecompany.com. The listing site has all the traffic and perhaps most of the links. The company site has all the branding signals. What is happening? The advantage of being an authority through content, traffic, SERP signals, etc., are not benefiting the company site and all of the brand signals of the company is not benefiting the listing site. You can attempt to brand the listing site, however, most of the signals that are required for a brand are what is termed RCS (real company sh_t) a term Google actually uses, are missing. What happens is that real advantages that all SEOs strive for are split between two sites and neither site can fully perform as it should unless combined. It is that simple.
