I did it myself in the first days that the sequence was available and came to the same conclusion that this is almost certainly natural in origin and it helps to point out that bats are the most genetically diverse among mammals representing around 1 in 5 mammal species. There aren't that many bat genome sequences that have been performed and so it isn't completely unexpected to find that the spike protein has recombined with a sequence that isn't known. You can however do the translation to amino acid sequence and then search just that spike sequence against known proteins in NCBI and find that it is quite close on the protein level to other known bat proteins, at least in part.

I don't think it is engineered, however it still could be a strain that was collected and analyzed at the Wuhan lab. I don't know if we will ever have the full story on that possibility.

Ah yes, I am familiar with that thread – I've been following it.

One thing does strike me as strange. The common ancestor here, RaTG13, was only sequenced and published by Shi's lab in Wuhan in late January. Despite supposedly being sequenced in 2013. Shi's Wuhan lab is the same one in question in this article regarding a potential leak.

Is this unusual for a lab to do, or is this common practice?

Others have asked this question in the Twitter thread you posted, but no one has responded so far as I can see. E.g:

https://twitter.com/LizSpecht/status/1223394697948753922 and https://twitter.com/LizSpecht/status/1223451393173803014