Suppose one pays 1 satoshi/byte for their transactions.
Will the confirmation of the two transaction below be different?
A) a transaction of 1 inputs and 1 output (~192 bytes)
B) a transaction of 1000 inputs and 1 output (~148044 bytes)
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Yes, but for a different reason than you think. ;)
Transactions bigger than 100,000 bytes are considered non-standard and won't be relayed by most nodes and probably not included by most miners in their block candidates.
Besides that, especially for a transaction paying a thrifty fee, a larger transaction might take longer to confirm. Block templates are by default populated by highest fee rate first as this maximizes revenue. It's more likely to have 192 bytes of block space left than 148,044 bytes after all transactions with higher fee rates have been considered. It's thus more likely for a bigger transaction to be delayed from inclusion in a block due to taking up more space.
The optimal transactions for miners to include in block is those with high fee and low volume. Transaction size is the major limit. In terms of lots of inputs, it should not be expensive since verifying signature is very easy and all the inputs are already in the pool of UTXO. So it really depends on miners' algorithm and other transactions. For example if the block has a very small size left and your transaction A is the best option then tx A gets lucky.