Introduction and Motherboard and PCIE layout /arrangement question

TL;DR;
Pros and cons of the PCIE x16 slot being in the 1st position (closest to the cpu) or the 2nd ( next one down) for SFF builds?

Long time lurker.

Thought ild say hello and ask some questions.

Got into SFF by accident. Mostly Play FPS games but go to lans with friends a 3 or 4 times a year and bust out COD2, flatout, age of mythology, AOE etc.
Went from Phanteks Enthoo Luxe Full Tower down to a Define mini C because i was sick of lugging the full tower to LANs and then there was no space for it. That made me catch the SFF bug hard and realise how much space is wasted on features on most cases i dont use any more. multiple 3.5Hdds, anything in a 5.25 bay, Crossfire / SLI
etc etc. Im making a rough conceptual CAD layouts for my ultimate case design as there is nothing close that suits my needs. I may modify a case to suit or maybe mock something up to see if i like it. Ill post some pictures in the concept and custom cases subform later today or tomorrow.

Im quite lucky and haven't spent alot on hardware as got the base machine 2nd hand from work for peanuts and added to that and have only brought a Graphics card PSU and case new over 3 builds. Rather than fully build a new PC i tend to do it in stages, Tick tock you could say. Case PSU. Next will be Mobo and CPU and then later GPU.
Went from X58 i7 920 with the GTX 970 in the luxe to the Define mini C. Then got a cheap I7 2600k system 3 years ago from work. But the Asrock Matx mobo cant OC past 4ghz so in what was my wifes P400 now with a full ATX P8Z68-V board, I7 2600k 1.33V for 4.7Ghz sitting under a H100i, 16gb ram 1600mhz with a gigabyte 1060 6gb powered by an EVGA G2 750W. Only just starting to feel the CPU is letting me down in FPS games.

I work as an electrical and instrumentation Draftsperson using autocad in 2D mostly but starting to learn fusion 360 at home for 3d printing stuff. Have no problems building my own PCs, overclocking etc. But new to ITX / SFF so here is the question.

I noticed some motherboards have the PCIE x16 slot in the 1st position (closest to the cpu) but most have it in the 2nd. I have noticed this in the past swapping cases but never been an Issue.

• As far as i can tell possible air cooling clearance issues if a GPU is populated in slot 1.
• But also noticed on the P-ATX because of the GPU riser cable goes if its in Slot 1 you can fit "taller" GPUs
  
  Am i missing any pros / cons or how it can effect SFF builds?
  
  Thinking of upgrading to a RYZEN 5 over the holidays and pretty much settled on MSI B450m Mortar Max or MSI B450I. Only thing there is i have to decide if i pay the premium for ITX so i can have more case options in the future or stick to mATX. I game with single GPU and will most likely use only one NVme drive and the extra I/O wont be used. So the ITX covers all my needs there. But thats just me needing to choose.

 

[Choidebu]

Pcie slot closest to cpu will always be the fastest and guaranteed to be full speed lanes. I don't know where you got that 'most' have their second slot to be 'the' x16 slot. For SLI/crossfire motherboards yes both are supposedly full speed, but it's also much depended on cpu or chipset. But the first one is always guaranteed to have the prioritised connection to either, simply because it is closer therefore easier to route.

 

[letarded]

Sorry i noticed when looking at mATX B450 boards that are available here the majority have either PCIE 1x slot or nothing at all in the first slot. gigabyte and asrock seem to be the main people, its not all the boards but more than 50%. My P8Z68-V also has 1x slot first and 16x slot 2nd.

im well aware the 1st full 16x pcie slot regardless if its in the 1st or 2nd placing from the cpu is wired 16x and the 2nd is 8x.

I was just wondering is there was any other hardware or case compatibility to look out for, especially with cases. But looking at more case reviews last couple of days i think its usually an issue.

 

[larkmaj]

One thing to keep in mind about the "premium for ITX" is that ITX boards typically come with wifi and bluetooth built-in while you'd have to add that on for an mATX. This seems to be the case on the MSI boards you've picked out as well. That $20+ for an M2 or PCIe wifi card makes up the difference.