When setting timing is Top Dead Center always the compression stroke?

There are, of course, two Top Dead Centers in every cycle, but in answer to the question I think you are asking, yes, any time a manual or procedure tells you to reference something to TDC, it always will mean compression TDC for cylinder #1, unless something very specific says otherwise.

Of course while the timing chain is removed, any TDC of the crank is as good as any other, and once you install the chain with the crank at a #1 and #4 TDC and the cams in the proper #1 compression position, well, you've just made that be #1 compression TDC.

 

This is a 2008 thread but I have a question regarding TDC. I used MrGasket video, aligned the two colored links on witness line of front timing gear and single color link on back gear witness line. I locked both cams per instruction and removed head. #1 and 4 were slightly below the highest travel … I would have to measure exact distance. I am assuming this is standard or am I mistaken?

 

This is what TDC looks like with an unbent connecting rod. If it doesn't get up this high for any rotation of the crankshaft, you've got a bent rod.
As long as you're within a couple of degrees of TDC, and you get the colored links into the right positions on the camshaft timing gear assembly, the camshaft timing sprocket, and the crankshaft timing sprocket, things will fall into place once you install and release the chain tensioner assembly.

 

Excellent! Thank you!