The reason why the 13k breakpoint will be better in 5.4 isn't necessarily because the 3k breakpoint will be more difficult to reach. Going from 3k to 13k gives a static boost to healing. Mastery, on the other hand, has DRs when you stack it. So, while 10k mastery might provide a 17% increase to healing in 5.3, it will likely go down to something like 15% in 5.4. In addition, the higher BP yields more throughput even WITHOUT taking the shorter GCDs and cast times into consideration. This means that, even if you have the same number of casts in a given amount of time from both breakpoints, the higher BP will still come out ahead. If you cast the same number of spells, it's impossible for one BP to use more mana than the other.
Now, in practice, the shorter GCD from nonrejuv spells is taken into consideration. If you chain cast, you're mana consumption will go up to a certain extent. However, with the higher BP, you do not need to chain cast to achieve more throughput than the lower BP. In other words, if you have mana problems with the 13k BP, pause for about a quarter of a second after the GCD is over every time you cast SM/WG/LB/dispel/RG. Your mana consumption will go down back to what it would be with the 3k BP, and you'll still be able to do more healing than you would with the 3k BP if you were chain casting. If you can't do that, then that's a playstyle issue and not a gearing issue.
Finally, having enough spirit should not be an issue in 5.4, even if you go for the higher BP. At current levels, you can both reach the 13k BP and still have enough secondary stats to get you to 12-13k spirit. That number will be even higher in 5.4.