There are several (easy) ways to bridge VLANs, but doing so, you're negating the primary purpose of VLANs. This is where the filtering issues comes into play, whether filtering by MACs and/or some L2 protocols. I.e. ideally, I presume, you only want the special L2 protocols to be able to communicate, directly, using L2 across VLANs.
I don't recall whether any Cisco equipment supports it, but I recall some vendors do support protocol based VLANs. For any that might, don't recall whether protocol could be purely L2. (NB: just did a quick search, protocol based VLANs support varies, per vendor, and Cisco does support protocol based VLANs on some of their SMB devices [other Cisco devices too?].)
The second issue, which I didn't get into, is whether these L2 protocols will operate totally independent of L3, which I'm guessing they do. Otherwise, they hosts will consider themselves on different networks and these specially L2 protocols may fail to operate correctly, if when you span/join their VLANs if they have IPs in different networks.
In summary, I still think this is a "maybe", again much depending on what your special L2 apps need and what your network can support.
Assuming there is one or more ways to do this, I'm sure you would want to compare the "cost" to do them, versus some of your other options, which for many reasons, you hope not need to pursue.
Your need is unusual enough, I think it unlikely anyone will pop up with, did exactly that too, just last week, doing this xxx.
BTW, this is the kind of project I often was asked to investigate, and so can say, it often requires a good bit of research, often some lab work (to confirm or correct possible implementations) and final analysis of best approach, which might lead you back to where you began.
