VLAN tunneling within one site?

This is an unusual one and, I'll be honest, one that will probably be a moot point by the time I get answers...but I'd like to understand the mechanics of how to make it work to increase my understanding.
Right now, I've just moved house and things are.... complicated! I've got a HAP AX2 behind a crappy 4G router on the window sill, hanging on to a mobile data signal. I've got another HAP AX2 in the office at the end of the garden. Between the two lies a Uniquiti Flex Mini that I can't (easily) reconfigure until I can get the server with the control software up and running.
I tried setting up a new VLAN between the AX2s so I can start trying to recreate some VPNs that aren't for general family use. I think the Flex Mini is filtering things in between - it used to be a workbenche switch. So I thought I'd try running them over an EoIP tunnel between the two to bypass the intermediary switch. I've probably over-thought it and created a second bridge for the EoIP tunnel and VLAN. All the docs are for a site to site situation rather than a local situation where the communication is direct over an untagged native VLAN.
In the next few days I should be able to start running cables so that it's Mikrotik end to end and I can get the server up to configure the switch that will longer be a problem...but I'd like to understand how this should be done as it feels like it should be easier than I'm making it!
Can anyone outline a topology of how to do this please?

Many thanks,
Gareth

If the switch between the routers does not transport VLANs in the TAG, the problem is probably MTU, you can change this value on both routers

If the switch between the routers does not transport VLANs in the TAG, the problem is probably MTU, you can change this value on both routers

This would only be an issue with ancient switch chips. More likely the switch configuration, additionally the Flex Mini is limited to ports either being trunk (all additional VLANs tagged) or access (a single untagged VLAN)

Is the flex mini just being used as an "extender" for a long run? Have you tried using the reset button to set it to factory default? There are some post on the ui forum that claim in factory default state it is vlan-transparent before being adopted. https://www.google.com/search?q=is+ubiquiti+flex+mini+vlan+transparent+before+being+adopted

If you have a dumb switch laying around, these are usually vlan-transparent, so they will forward the ethernet frames just as they were received, if tagged they will remain tagged, if no tag they will remain untagged. The switch just doesn't treat ethertype 0x8100 as being special in any way. (even most old routers have a built in switch that should be vlan transparent, but if you use it be sure to disable the dhcp server or it will cause havoc).

Most plug an play unmanaged switches produced in the last 15 years (i.e. generic consumer ethernet switches, e.g. I have a Tenda SG105 5 port Gb switch I got on sale at MicroCenter for under $10 that is vlan transparent) will pass at least baby giant packets, many will pass 8K + byte packets. So MTU is very unlikey to fix the problem in my opinion.

It doesn't need a second bridge, you could add the EoIP interface to the existing bridge either with a PVID which matches the /interface vlan for CPU access if you are transporting a single VLAN, or set to tagged-only and the memberships set under /interface bridge vlan if you are transporting several VLANs. Make sure the EoIP MTU is set to 1500.

The flex mini was previously set up for a trunked port and a couple of different VLANs. I'd been trying not to wipe stuff purely because I intended to drop it all back in once I had my internet connection installed. Can't reconfigure the flex mini without the controller software which is on the server that turns out not to have survived (at present) the move.
Yes, the flex mini was joining some segments of LAN - 4G router on the window sill with a cable back to the flex mini. Some random cables to places from the flex mini.

I've not got as far as running new network cables to a central place so the flex mini is currently out of the picture. Mikrotik CRS320 at the centre and a variety of HAP AX2s about the place for wifi...because the UAP-AC-HD didn't survive the journey either for some reason - no obvious damage either.

This was more of an interest question as things have changed massively already. In my head, this should have been a quick and easy temporary fix but I didn't get it working. I really wanted to know what I'd done wrong so that I can maybe use it if I find something in the future that 'needs' it.

@tdw Cheers, I'll try and set something up on a couple of test boxes once I get a chance - chaos after moving house!

and

If the flex mini had only a single trunk port configured, it wouldn't be able to pass tagged traffic through it, because by definition at least one of the ports would have been configured as an access port, and that won't pass any tagged traffic.

If it previously had an Access Point with multiple SSIDs attached to different vlans, then if you had used the two ports that were configured as trunks, then if those two flex mini trunk ports were connected between the two hAPax2 devices, I would have expected that to work.

Definitely makes sense.
The AP was previous hanging off a Mikrotik CRS320, running off PoE. The odd thing is that it doesn't show as a PoE load on the 320 now. Run it off an injector and it's fine. Switch the 320's port to Always On and it works...it just makes me nervous for anything else that might ever get plugged into that port. I can only assume that the resistors (IIRC) that indicate there's a PoE load, have failed somehow. Weird.