your questions are very broad and general, I will try to provide some answers as I have designed boards up to 20GHz.
as to why multi-layer RF PCBs? Contrary to many years ago more and more products require the integration some of the RF functionality to be combined with non-RF functions onto a single PCB due to cost pressure dictated by the market. Thus, simply using the most expensive, high end RF PCB material, do a 2 layer design, shield it with an AL shield is often simply too expensive. If your product supports that cost/margin, go for it...
The moment you need more than just RF on a PCB (uC, FPGA, or many analog functions) you need more than 2 layers. So the question becomes, when and how do you decide that 4 (or more) layer FR4 can't be used due to RF requirements?
One question to consider is the following: Do you do discrete RF design, meaning you have many individual circuits, components that create an RF system, thus you need to route RF signals from RF block to RF block, or do you have a very highly integrated RF transceiver IC that only has one high frequency RF input that needs to be connected to a filter and an antenna, because all other signals out of that RF chip are base-band signals? If the latter is the case you will be surprised for how long you can get away with FR4, because you only need one RF trace from the chip to the antenna and you keep that trace extremely short. We once did a 10GHz design on FR4 and got away with it (extreme cost pressure of the target market). We kept the one RF line extremely short, routed the signal into the RF chip and the remaining signals were base-band (low freq. signals) so that worked out ok. (The target market was low cost consumer electronics.)
If you do discrete RF design, but need more than 2 layers you can chose a sandwiched PCB stack up like the one shown below. You could use RF material (Rogers 4350 for example) for layer 1-2 and 3-4 and use FR4 like material in between (from 2 to 3). More layers would scale accordingly, thus for an 8 layer board you could use RF material for layers 1,2 and 7,8 and FR4 for everything in between.
In this case keep all RF traces on the top, use layer 2 as RF ground and do nothing else on that layer! Layer 3 could be power and some routing and layer 4 (bottom) could be used for digital routing and placing non RF components on the bottom side. With careful layout shielding techniques you can achieve very good isolation (> 120dB) between top and bottom layer. You can design boards where you run a uC with 20MHz xtal clock on the bottom side and with proper shielding within the PCB you will have a hard time even finding the clock from the bottom side on the top, unless you use very sensitive equipment. In addition you can still design a mechanical Al RF shield that is mounted to the top side of the RF section of the PCB to shield circuits located on the same side from each other.
Vias: Depending on the density of your board, you may run into issues if you want to avoid blind vias for cost reasons. If you route your digital and supply signals from the bottom side (lets say from layer 4 to 3) using a thru via, the end of that via will go all the way to the RF layer 1. The signal contained in that via ("only" to be routed from 4-3) will couple into the RF ground plane in layer 2 and (if applicable) layer 1. To avoid that you can use blind vias if you can justify the cost increase. If possible I would try to avoid routing RF signals thru several layers and keep them on the same layer.
Multiple high speed clock signals: If your design requires many GHz clock signals it is likely not possible to keep all the signals on the top side, in this case you will have to route the signals over several layers, you have to be very careful and make sure your matching and shielding is sufficient. In this case the PCB stack will be different and more expensive.
Development time and schedule: You also need to consider whether your schedule (and cost constraints) permits spinning the board several times to get the required RF performance in the presence of digital signals. You may have to use special tools (EM simulators) which can't be justified all the time (cost of the tool and the experience needed to use such a tool).
There is no general answer because there are too many variables/requirements to consider.... but I hope this answers some of your questions.