@Thespoon
I have similar size house with basement and two floors, and Deco mesh with M9 Plus units, running in AP mode. The following is based on my experience.
What you plan will work, and if you want good WiFi 5GHz coverage you should have one Deco on each floor. If your house has wooden floors (allowing good WiFi signal penetration) and you are OK with just 2.4GHz signal, two Deco units might be enough - but you'll be disappointed by WiFi speeds. I recommend you go with three, one per floor (including basement).
I bought M9 Plus, because I wanted good wireless backhaul that is available in tri-band mesh systems. I paid premium for M9 to have that, comparing to other Deco models. In your case, M9 dedicated wireless backhaul won't give you any benefit, as you will wire all your Deco units.
Are there any other reasons you plan to use M9, instead of less expensive M4 or M5 with similar WiFi specs?
For your home network, unless your budget is really tight or you need something specific available in M9 only, I would recommend to consider Deco X20 or X60. They support WiFi6, which means future proof for your home WiFi. Deco M-series is only up to WiFi5. Nothing wrong with it, but WiFi6 devices could do better with home network you have if they connect to X20/X60.
I don't know where you live, but right now, as I type this post, in Canada where I live I could order 3-pack X60 (it is on sale) on Amazon for about the same price as 3-pack M9 Plus (regular price). I can also get 3-pack X20 for same price as 3-pack M9 Plus.
If you could find 3-pack X60 for same or very close price as M9 Plus, I would strongly recommend X60s and to buy them right away, while on sale. If X60s are not on sale, check X20s prices.
Specs for different Deco models can be found in this FAQ article: What are the differences between different models of Deco?
In regard to your network diargam and questions.
> "the Wi-FI will be generated from the modem/router installed on the basement"
That's not how Deco mesh works, if you assumed that Deco will rebroadcast router WiFi signal. Instead, you will turn off WiFi on modem/router. Modem/router will manage your home network, Deco mesh will provide and manage your WiFi. You will configure WiFi network in Deco app, and you can use same SSID/password that was on your modem/router WiFi, so that mobile devices can seamlessly connect to Deco mesh after you turn off router WiFi.
>Does TP-LINK have media converters from Fiber to RJ, able to support 1 or 2 GBPS?
Can't answer that. Just one recommendation: Deco M4/M5/M9/X20/X60 Ethernet port is 1 gigabit, so if there is substantial price difference between 1 and 2 Gbps media converters, don't waste your money on 2Gbps.
>M9 PLUS has 2 Ethernet Ports, considering my setup, the first port will be plugged to the router. May I use the second RJ port for plugging a PC desktop
Yes, you can use second port to plug any device that uses Ethernet connection, which includes desktop PC. This is one of the Deco features I really like, and use.
>When the Deco works in Access Point, at home you can always see just one network
Wireless device will see one Deco network SSID and should seamlessly roam between Deco units, which is the point of mesh system. Configuring device to connect to Deco mesh WiFi is same as configuring it to connect to a single WiFi router.
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If you have more questions or want me to clarify what I said, feel free to ask.