There are lots of reasons why a desktop would be faster than a laptop, even with the same "notional" CPU. The TDP of a laptop is never going to match that of a desktop. Laptop RAM is slower than desktop RAM. Motherboard design and chipsets make trade-offs for laptops. I'm sure someone more knowledgeable than myself could list many other reasons, too. How much impact each factor has will vary from task to task. I'd guess Xcode builds are dominated by single-core performance, memory bandwidth, and I/O bandwidth.
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I mean this in the best way possible, but I'm not sure you really know much about what you're saying. The CPU can draw way more power than the TDP if allowed by the thermals. And one core running full tilt won't remotely hit the TDP. On my machine its hitting like 25-30W with a single thread running at 5GHz. When all threads kick on, it can spike to 90-100W draw. Anyway between the 9900K and the 9980HK, the memory bandwidth is the same, 41.8 GB/s, duel channel, bus speed the same, cache the same, max turbo the same, I/O access via PCIe or SATA is going to the be same. Its not like these things just get slower because its a laptop. I'd bet this is a software difference. What OS is your desktop? Maybe this app is doing some thing strange to run on macOS. Maybe even its configured to run better on an older MacOS version on your 2013?
Sure, it's definitely an individual choice, and depends on one's comfort level with performing such upgrades and the various risks involved. For me it would be a no brainer - I think the risks are minimal and the cost savings are huge - although I would obviously test the machine thoroughly first before going ahead, in case there was a manufacturing fault that needed attention.
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What if the problem encountered happens 6 months in? Say the mother board is the culprit, but you have aftermarket ram and boot drive, what do you think Lenovo is going to say you do?
As pointed out in an earlier post, you can do it for *much* cheaper than 3K by upgrading the RAM and SSD yourself, something you can do with most PC laptops, but cannot currently do with any MacBook.
For example, Apple charges $600 for the 2TB SSD upgrade. You can buy a Sabrent 2TB NVMe SSD for $250 and sell a 512GB SSD for $70, so an equivalent upgrade to a PC laptop can be done for $180.
Apple charges $400 for the 32GB RAM upgrade, from 16GB. You can buy 32GB DDR4 2666MHz RAM for $115 and sell 16GB for around $70, so that upgrade should cost $35.
So we've just saved $420 + $365 = $785 on upgrades alone. But those upgrade prices are on top of an already very high base price. During a good sale, the Lenovos start around $1200. The base MBP 16" will set you back $2400, a full $1200 more. $1200 + $785 = $1985.
Yes, Lenovo and Dell overcharge for upgrades too, but the point is, their machines are user upgradeable so a smart buyer can do it themselves, to save money.
The Thinkpad X1 Extreme Gen 2 for $1200, even the stripped down model? Link or didn't happen. Cheapest I see is roughly what it is currently, $1475, vs cheapest sale about $100 less. I think you're looking at gen 1....
I don't think you're going to sell 16GB of RAM as a naked stick or two pulled out of your machine for $70. You can get 16GB DDR4 modules for like $60 new (after all that's what your $115 per 32GB is assuming). Same for the SSD. A used drive without a box... $50. I mean, this is peanuts, I think the bigger issue is that you should probably keep those anyway incase you have a problem and need to ship the computer back to Lenovo. At the very least, get it through its warranty on the manufacture installed equipment. If you want to try to add things, like a second stick or drive, that's easier. And hey, if you're complaining about not being able to upgrade and fix the machine as you go, out of support, that would make a heck of a lot more sense and that's something I very much regret. I loved my 2011 MacBook Pro for that. Changed the battery twice, upgrade the ram, took out the ODD, moved the HDD in there, put in an SSD. I wish I could buy a modern Mac like that.... well, I could skip the ODD.
Anyway, point is, for a similarly spec-ed machine fully supported by the manufacture you're looking at maybe a 10-20% price gap. Some call this the Apple tax. Look, I'm not going to argue that Apple computers aren't expensive. They are, but its often overstated and usually because of the exact things you're doing, throwing away or neglecting certain aspects that have value, like support. Its pure spec sheet comparisons. You can cobble together a lot of stuff for cheap and build a computer from scratch, but you are then your own support. When something fails, you have to track down what it was and contact each vendor and convince them its their problem, not some other component's problem. Its all your time. Here, I can clone a machine in a few hours and be back on my feet while the old machine sails off. I can't get the OS anywhere else either, not a supported one anyway. And this is coming from a guy that's done a home built computer and made it run OS X. I eventually gave up and put windows on it, but it worked, sort of. I have also played support on two linux servers at work, configured and built a server for another small company. I've done this for a job. And that's kind of the point, its a job. Its your time. $3000 for "it just works" vs $2400 for the specs match now lets hope it holds together...