Learn Finnish: Pajassako lasinpuhallus on parhaillaan meneillään? - Is it in the workshop that the glassblowing is currently underway?

By attaching the question clitic -ko to the location pajassa (in the workshop) and moving it to the front, you create a contrastive focus. The question assumes glassblowing is happening, but asks specifically if it is happening in the workshop as opposed to somewhere else.

Would the sentence mean the same thing if it started with the verb Onko?

No, the emphasis would be entirely different. If you asked Onko lasinpuhallus parhaillaan meneillään pajassa?, it would be a neutral yes/no question asking if the action is happening at all. Fronting Pajassako puts the interrogation spotlight exclusively on the location.

The word parhaillaan translates to currently here, but what is its literal structure?

It is built from the adjective paras (best) in the adessive plural form parhailla-, plus the third-person possessive suffix -an. Literally it means at its best, which is used idiomatically in Finnish to indicate that an action is currently in full swing.

How does meneillään function here alongside parhaillaan?

Meneillään means underway or in progress. It is built from the verb mennä (to go) using the plural adessive ending -eillä and the possessive suffix -än. While parhaillaan alone can mean currently, using both together is a very common idiom to emphasize that a continuous event is actively taking place right this second.